Starting phenix.real_space_refine on Wed Apr 8 01:27:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zlq_11272/04_2026/6zlq_11272.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zlq_11272/04_2026/6zlq_11272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zlq_11272/04_2026/6zlq_11272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zlq_11272/04_2026/6zlq_11272.map" model { file = "/net/cci-nas-00/data/ceres_data/6zlq_11272/04_2026/6zlq_11272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zlq_11272/04_2026/6zlq_11272.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 16 7.16 5 S 96 5.16 5 C 21156 2.51 5 N 6081 2.21 5 O 6474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 275 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33823 Number of models: 1 Model: "" Number of chains: 38 Chain: "Z" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "A" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "C" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "E" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "G" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "H" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "I" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "J" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "K" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "L" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "M" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "N" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "O" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "P" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "Q" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "R" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "S" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "T" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "U" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "V" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "W" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "B" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1413 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 1 Chain: "D" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "F" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6624 SG CYS G 127 94.590 35.355 94.952 1.00 49.43 S ATOM 3812 SG CYS C 127 32.999 92.115 94.710 1.00 51.15 S ATOM 33401 SG CYS F 127 34.999 96.220 93.578 1.00 51.16 S ATOM 8037 SG CYS H 127 92.337 32.586 30.226 1.00 49.75 S ATOM 22132 SG CYS R 127 95.960 35.310 31.733 1.00 49.70 S ATOM 29176 SG CYS W 127 94.868 31.421 34.162 1.00 49.03 S ATOM 9450 SG CYS I 127 35.297 94.965 30.333 1.00 48.26 S ATOM 24944 SG CYS T 127 31.599 92.306 31.715 1.00 47.82 S ATOM 15081 SG CYS M 127 32.683 96.197 34.174 1.00 48.96 S ATOM 24944 SG CYS T 127 31.599 92.306 31.715 1.00 47.82 S ATOM 10856 SG CYS J 127 92.271 95.991 31.720 1.00 48.41 S ATOM 20726 SG CYS Q 127 94.996 92.349 30.226 1.00 48.38 S ATOM 30589 SG CYS B 127 96.337 92.604 93.409 1.00 50.22 S ATOM 19313 SG CYS P 127 96.110 94.896 34.196 1.00 48.70 S ATOM 20726 SG CYS Q 127 94.996 92.349 30.226 1.00 48.38 S ATOM 12262 SG CYS K 127 31.483 32.751 34.149 1.00 47.46 S ATOM 23538 SG CYS S 127 35.389 31.666 31.627 1.00 46.91 S ATOM 12262 SG CYS K 127 31.483 32.751 34.149 1.00 47.46 S ATOM 26357 SG CYS U 127 32.566 35.215 30.125 1.00 47.87 S ATOM 6624 SG CYS G 127 94.590 35.355 94.952 1.00 49.43 S ATOM 5218 SG CYS E 127 92.355 94.898 95.060 1.00 49.62 S ATOM 30589 SG CYS B 127 96.337 92.604 93.409 1.00 50.22 S ATOM 1000 SG CYS Z 127 35.211 32.539 95.408 1.00 48.90 S ATOM 33401 SG CYS F 127 34.999 96.220 93.578 1.00 51.16 S Time building chain proxies: 7.15, per 1000 atoms: 0.21 Number of scatterers: 33823 At special positions: 0 Unit cell: (128.7, 128.7, 126.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 16 26.01 S 96 16.00 O 6474 8.00 N 6081 7.00 C 21156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.2 seconds 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7842 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'Z' and resid 10 through 38 removed outlier: 4.123A pdb=" N ALA Z 16 " --> pdb=" O GLU Z 12 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN Z 18 " --> pdb=" O GLU Z 14 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE Z 38 " --> pdb=" O LEU Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 71 Processing helix chain 'Z' and resid 72 through 74 No H-bonds generated for 'chain 'Z' and resid 72 through 74' Processing helix chain 'Z' and resid 92 through 121 Processing helix chain 'Z' and resid 123 through 156 removed outlier: 3.948A pdb=" N LEU Z 135 " --> pdb=" O GLU Z 131 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP Z 136 " --> pdb=" O SER Z 132 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS Z 137 " --> pdb=" O HIS Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 170 through 179 removed outlier: 3.619A pdb=" N GLU Z 176 " --> pdb=" O GLU Z 172 " (cutoff:3.500A) Processing helix chain 'Z' and resid 179 through 187 Processing helix chain 'A' and resid 10 through 38 removed outlier: 4.241A pdb=" N ALA A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 71 Processing helix chain 'A' and resid 92 through 121 removed outlier: 3.530A pdb=" N ASN A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 134 through 156 Processing helix chain 'A' and resid 170 through 179 Processing helix chain 'A' and resid 179 through 188 Processing helix chain 'C' and resid 13 through 38 removed outlier: 3.579A pdb=" N ASN C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 74 removed outlier: 3.804A pdb=" N ASP C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 122 removed outlier: 3.535A pdb=" N ASN C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 134 through 156 Processing helix chain 'C' and resid 170 through 179 removed outlier: 3.714A pdb=" N GLU C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 188 removed outlier: 3.690A pdb=" N SER C 188 " --> pdb=" O GLY C 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 39 removed outlier: 4.175A pdb=" N ALA E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 71 Processing helix chain 'E' and resid 92 through 121 removed outlier: 3.519A pdb=" N ASN E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 156 removed outlier: 3.952A pdb=" N LEU E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASP E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS E 137 " --> pdb=" O HIS E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 179 removed outlier: 3.721A pdb=" N GLU E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 188 Processing helix chain 'G' and resid 10 through 39 removed outlier: 4.183A pdb=" N ALA G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN G 18 " --> pdb=" O GLU G 14 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP G 39 " --> pdb=" O GLY G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 71 Processing helix chain 'G' and resid 72 through 74 No H-bonds generated for 'chain 'G' and resid 72 through 74' Processing helix chain 'G' and resid 92 through 121 removed outlier: 3.509A pdb=" N ASN G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 156 removed outlier: 3.945A pdb=" N LEU G 135 " --> pdb=" O GLU G 131 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP G 136 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 137 " --> pdb=" O HIS G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.726A pdb=" N GLU G 176 " --> pdb=" O GLU G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 187 Processing helix chain 'H' and resid 10 through 38 removed outlier: 3.912A pdb=" N ALA H 16 " --> pdb=" O GLU H 12 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 71 Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 92 through 122 removed outlier: 3.529A pdb=" N ASN H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 134 Processing helix chain 'H' and resid 134 through 156 Processing helix chain 'H' and resid 170 through 179 removed outlier: 3.798A pdb=" N GLU H 176 " --> pdb=" O GLU H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 187 Processing helix chain 'I' and resid 10 through 38 removed outlier: 4.191A pdb=" N ALA I 16 " --> pdb=" O GLU I 12 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN I 18 " --> pdb=" O GLU I 14 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE I 38 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 71 Processing helix chain 'I' and resid 72 through 74 No H-bonds generated for 'chain 'I' and resid 72 through 74' Processing helix chain 'I' and resid 92 through 122 Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 134 through 156 Processing helix chain 'I' and resid 170 through 179 removed outlier: 3.797A pdb=" N GLU I 176 " --> pdb=" O GLU I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 187 Processing helix chain 'J' and resid 10 through 15 removed outlier: 3.523A pdb=" N ALA J 15 " --> pdb=" O THR J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 39 removed outlier: 3.571A pdb=" N ASN J 22 " --> pdb=" O ASN J 18 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE J 38 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP J 39 " --> pdb=" O GLY J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 71 Processing helix chain 'J' and resid 92 through 121 Processing helix chain 'J' and resid 123 through 156 removed outlier: 3.942A pdb=" N LEU J 135 " --> pdb=" O GLU J 131 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASP J 136 " --> pdb=" O SER J 132 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS J 137 " --> pdb=" O HIS J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 179 removed outlier: 3.694A pdb=" N GLU J 176 " --> pdb=" O GLU J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 188 Processing helix chain 'K' and resid 10 through 38 removed outlier: 3.832A pdb=" N ALA K 16 " --> pdb=" O GLU K 12 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN K 18 " --> pdb=" O GLU K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 71 Processing helix chain 'K' and resid 72 through 74 No H-bonds generated for 'chain 'K' and resid 72 through 74' Processing helix chain 'K' and resid 92 through 121 Processing helix chain 'K' and resid 123 through 156 removed outlier: 3.963A pdb=" N LEU K 135 " --> pdb=" O GLU K 131 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASP K 136 " --> pdb=" O SER K 132 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS K 137 " --> pdb=" O HIS K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 179 removed outlier: 3.766A pdb=" N GLU K 176 " --> pdb=" O GLU K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 187 Processing helix chain 'L' and resid 10 through 38 removed outlier: 4.051A pdb=" N ALA L 16 " --> pdb=" O GLU L 12 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN L 18 " --> pdb=" O GLU L 14 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 73 Processing helix chain 'L' and resid 92 through 122 Processing helix chain 'L' and resid 123 through 134 Processing helix chain 'L' and resid 134 through 155 Processing helix chain 'L' and resid 170 through 179 removed outlier: 3.843A pdb=" N GLU L 176 " --> pdb=" O GLU L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 187 Processing helix chain 'M' and resid 10 through 38 removed outlier: 3.874A pdb=" N ALA M 16 " --> pdb=" O GLU M 12 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN M 18 " --> pdb=" O GLU M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 71 Processing helix chain 'M' and resid 72 through 74 No H-bonds generated for 'chain 'M' and resid 72 through 74' Processing helix chain 'M' and resid 92 through 121 Processing helix chain 'M' and resid 123 through 156 removed outlier: 3.965A pdb=" N LEU M 135 " --> pdb=" O GLU M 131 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASP M 136 " --> pdb=" O SER M 132 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS M 137 " --> pdb=" O HIS M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 179 removed outlier: 3.766A pdb=" N GLU M 176 " --> pdb=" O GLU M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 188 removed outlier: 3.541A pdb=" N SER M 188 " --> pdb=" O GLY M 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 15 Processing helix chain 'N' and resid 15 through 38 Processing helix chain 'N' and resid 45 through 73 removed outlier: 3.828A pdb=" N ASP N 72 " --> pdb=" O GLU N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 121 Processing helix chain 'N' and resid 123 through 134 Processing helix chain 'N' and resid 134 through 155 Processing helix chain 'N' and resid 170 through 179 removed outlier: 3.877A pdb=" N GLU N 176 " --> pdb=" O GLU N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 188 removed outlier: 3.613A pdb=" N SER N 188 " --> pdb=" O GLY N 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 38 removed outlier: 4.188A pdb=" N ALA O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN O 18 " --> pdb=" O GLU O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 73 Processing helix chain 'O' and resid 92 through 122 Processing helix chain 'O' and resid 123 through 134 Processing helix chain 'O' and resid 134 through 156 removed outlier: 3.548A pdb=" N ARG O 154 " --> pdb=" O THR O 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 179 removed outlier: 3.865A pdb=" N GLU O 176 " --> pdb=" O GLU O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 188 Processing helix chain 'P' and resid 10 through 38 removed outlier: 3.835A pdb=" N ALA P 16 " --> pdb=" O GLU P 12 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN P 18 " --> pdb=" O GLU P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 71 Processing helix chain 'P' and resid 72 through 74 No H-bonds generated for 'chain 'P' and resid 72 through 74' Processing helix chain 'P' and resid 92 through 121 Processing helix chain 'P' and resid 123 through 156 removed outlier: 3.964A pdb=" N LEU P 135 " --> pdb=" O GLU P 131 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP P 136 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS P 137 " --> pdb=" O HIS P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 170 through 179 removed outlier: 3.774A pdb=" N GLU P 176 " --> pdb=" O GLU P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 188 Processing helix chain 'Q' and resid 10 through 40 removed outlier: 3.910A pdb=" N ALA Q 16 " --> pdb=" O GLU Q 12 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN Q 18 " --> pdb=" O GLU Q 14 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE Q 38 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 71 Processing helix chain 'Q' and resid 72 through 74 No H-bonds generated for 'chain 'Q' and resid 72 through 74' Processing helix chain 'Q' and resid 92 through 121 removed outlier: 3.506A pdb=" N ASN Q 106 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 134 Processing helix chain 'Q' and resid 134 through 156 removed outlier: 3.574A pdb=" N HIS Q 148 " --> pdb=" O LYS Q 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 170 through 179 removed outlier: 3.825A pdb=" N GLU Q 176 " --> pdb=" O GLU Q 172 " (cutoff:3.500A) Processing helix chain 'Q' and resid 179 through 187 Processing helix chain 'R' and resid 10 through 15 Processing helix chain 'R' and resid 15 through 38 removed outlier: 3.523A pdb=" N PHE R 38 " --> pdb=" O LEU R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 71 Processing helix chain 'R' and resid 72 through 74 No H-bonds generated for 'chain 'R' and resid 72 through 74' Processing helix chain 'R' and resid 92 through 122 Processing helix chain 'R' and resid 123 through 156 removed outlier: 3.952A pdb=" N LEU R 135 " --> pdb=" O GLU R 131 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASP R 136 " --> pdb=" O SER R 132 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS R 137 " --> pdb=" O HIS R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 179 removed outlier: 3.704A pdb=" N GLU R 176 " --> pdb=" O GLU R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 188 Processing helix chain 'S' and resid 10 through 38 removed outlier: 4.081A pdb=" N ALA S 16 " --> pdb=" O GLU S 12 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN S 18 " --> pdb=" O GLU S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 71 Processing helix chain 'S' and resid 72 through 74 No H-bonds generated for 'chain 'S' and resid 72 through 74' Processing helix chain 'S' and resid 92 through 121 removed outlier: 3.523A pdb=" N ASN S 106 " --> pdb=" O ALA S 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 156 removed outlier: 3.928A pdb=" N LEU S 135 " --> pdb=" O GLU S 131 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP S 136 " --> pdb=" O SER S 132 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS S 137 " --> pdb=" O HIS S 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 170 through 179 removed outlier: 3.732A pdb=" N GLU S 176 " --> pdb=" O GLU S 172 " (cutoff:3.500A) Processing helix chain 'S' and resid 179 through 187 Processing helix chain 'T' and resid 10 through 40 removed outlier: 4.131A pdb=" N ALA T 16 " --> pdb=" O GLU T 12 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN T 18 " --> pdb=" O GLU T 14 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP T 39 " --> pdb=" O GLY T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 71 Processing helix chain 'T' and resid 72 through 74 No H-bonds generated for 'chain 'T' and resid 72 through 74' Processing helix chain 'T' and resid 92 through 121 removed outlier: 3.560A pdb=" N ASN T 106 " --> pdb=" O ALA T 102 " (cutoff:3.500A) Processing helix chain 'T' and resid 123 through 156 removed outlier: 3.944A pdb=" N LEU T 135 " --> pdb=" O GLU T 131 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASP T 136 " --> pdb=" O SER T 132 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS T 137 " --> pdb=" O HIS T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 170 through 179 removed outlier: 3.688A pdb=" N GLU T 176 " --> pdb=" O GLU T 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 179 through 187 Processing helix chain 'U' and resid 10 through 38 removed outlier: 4.132A pdb=" N ALA U 16 " --> pdb=" O GLU U 12 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN U 18 " --> pdb=" O GLU U 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE U 38 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 71 Processing helix chain 'U' and resid 72 through 74 No H-bonds generated for 'chain 'U' and resid 72 through 74' Processing helix chain 'U' and resid 92 through 121 removed outlier: 3.550A pdb=" N ASN U 106 " --> pdb=" O ALA U 102 " (cutoff:3.500A) Processing helix chain 'U' and resid 123 through 134 Processing helix chain 'U' and resid 134 through 156 removed outlier: 3.594A pdb=" N LYS U 143 " --> pdb=" O VAL U 139 " (cutoff:3.500A) Processing helix chain 'U' and resid 170 through 179 removed outlier: 3.760A pdb=" N GLU U 176 " --> pdb=" O GLU U 172 " (cutoff:3.500A) Processing helix chain 'U' and resid 179 through 187 Processing helix chain 'V' and resid 10 through 15 removed outlier: 3.522A pdb=" N ALA V 15 " --> pdb=" O THR V 11 " (cutoff:3.500A) Processing helix chain 'V' and resid 15 through 40 Processing helix chain 'V' and resid 45 through 72 removed outlier: 3.899A pdb=" N ASP V 72 " --> pdb=" O GLU V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 92 through 122 Processing helix chain 'V' and resid 123 through 134 Processing helix chain 'V' and resid 134 through 155 Processing helix chain 'V' and resid 170 through 179 removed outlier: 3.836A pdb=" N GLU V 176 " --> pdb=" O GLU V 172 " (cutoff:3.500A) Processing helix chain 'V' and resid 179 through 187 Processing helix chain 'W' and resid 10 through 38 removed outlier: 3.854A pdb=" N ALA W 16 " --> pdb=" O GLU W 12 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN W 18 " --> pdb=" O GLU W 14 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 71 removed outlier: 3.727A pdb=" N GLU W 57 " --> pdb=" O ARG W 53 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU W 58 " --> pdb=" O GLU W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 92 through 121 Processing helix chain 'W' and resid 123 through 156 removed outlier: 3.945A pdb=" N LEU W 135 " --> pdb=" O GLU W 131 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP W 136 " --> pdb=" O SER W 132 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS W 137 " --> pdb=" O HIS W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 170 through 179 removed outlier: 3.784A pdb=" N GLU W 176 " --> pdb=" O GLU W 172 " (cutoff:3.500A) Processing helix chain 'W' and resid 179 through 188 Processing helix chain 'B' and resid 10 through 38 removed outlier: 4.088A pdb=" N ALA B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 73 removed outlier: 3.835A pdb=" N GLU B 57 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 64 " --> pdb=" O ARG B 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 122 removed outlier: 3.504A pdb=" N ASN B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 removed outlier: 3.647A pdb=" N GLU B 131 " --> pdb=" O CYS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.779A pdb=" N GLU B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 187 Processing helix chain 'D' and resid 10 through 38 removed outlier: 4.175A pdb=" N ALA D 16 " --> pdb=" O GLU D 12 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 73 removed outlier: 3.669A pdb=" N GLU D 57 " --> pdb=" O ARG D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 121 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 134 through 156 Processing helix chain 'D' and resid 170 through 179 Processing helix chain 'D' and resid 179 through 186 Processing helix chain 'F' and resid 10 through 38 removed outlier: 4.088A pdb=" N ALA F 16 " --> pdb=" O GLU F 12 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN F 18 " --> pdb=" O GLU F 14 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE F 38 " --> pdb=" O LEU F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 73 Processing helix chain 'F' and resid 92 through 122 removed outlier: 3.692A pdb=" N LEU F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 133 removed outlier: 3.902A pdb=" N GLU F 131 " --> pdb=" O CYS F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 156 removed outlier: 3.727A pdb=" N LYS F 137 " --> pdb=" O HIS F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 179 removed outlier: 3.816A pdb=" N GLU F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 188 removed outlier: 3.606A pdb=" N SER F 188 " --> pdb=" O GLY F 184 " (cutoff:3.500A) 2600 hydrogen bonds defined for protein. 7800 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: 6.17 Time building geometry restraints manager: 3.38 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: 11802 1.34 - 1.46: 7661 1.46 - 1.58: 14728 1.58 - 1.71: 0 1.71 - 1.83: 168 Bond restraints: 34359 Sorted by residual: bond pdb=" CB VAL J 21 " pdb=" CG1 VAL J 21 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.70e+00 bond pdb=" CB VAL V 155 " pdb=" CG2 VAL V 155 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.38e+00 bond pdb=" CB THR F 30 " pdb=" CG2 THR F 30 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.33e+00 bond pdb=" CB VAL N 155 " pdb=" CG2 VAL N 155 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" N VAL N 155 " pdb=" CA VAL N 155 " ideal model delta sigma weight residual 1.474 1.451 0.023 1.57e-02 4.06e+03 2.14e+00 ... (remaining 34354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 44412 1.66 - 3.32: 1461 3.32 - 4.98: 202 4.98 - 6.63: 48 6.63 - 8.29: 23 Bond angle restraints: 46146 Sorted by residual: angle pdb=" C LEU T 178 " pdb=" N THR T 179 " pdb=" CA THR T 179 " ideal model delta sigma weight residual 122.17 117.98 4.19 1.54e+00 4.22e-01 7.40e+00 angle pdb=" C LEU R 178 " pdb=" N THR R 179 " pdb=" CA THR R 179 " ideal model delta sigma weight residual 122.17 118.04 4.13 1.54e+00 4.22e-01 7.20e+00 angle pdb=" C LEU K 178 " pdb=" N THR K 179 " pdb=" CA THR K 179 " ideal model delta sigma weight residual 122.17 118.06 4.11 1.54e+00 4.22e-01 7.14e+00 angle pdb=" C ARG C 73 " pdb=" N GLY C 74 " pdb=" CA GLY C 74 " ideal model delta sigma weight residual 123.44 120.47 2.97 1.19e+00 7.06e-01 6.22e+00 angle pdb=" N ARG J 19 " pdb=" CA ARG J 19 " pdb=" C ARG J 19 " ideal model delta sigma weight residual 113.18 110.28 2.90 1.21e+00 6.83e-01 5.76e+00 ... (remaining 46141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 17409 17.99 - 35.98: 2534 35.98 - 53.97: 676 53.97 - 71.96: 90 71.96 - 89.95: 15 Dihedral angle restraints: 20724 sinusoidal: 8625 harmonic: 12099 Sorted by residual: dihedral pdb=" CA ASP D 128 " pdb=" C ASP D 128 " pdb=" N PHE D 129 " pdb=" CA PHE D 129 " ideal model delta harmonic sigma weight residual 180.00 155.52 24.48 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA HIS M 133 " pdb=" C HIS M 133 " pdb=" N TYR M 134 " pdb=" CA TYR M 134 " ideal model delta harmonic sigma weight residual -180.00 -159.93 -20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA HIS J 133 " pdb=" C HIS J 133 " pdb=" N TYR J 134 " pdb=" CA TYR J 134 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 20721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3249 0.037 - 0.073: 1314 0.073 - 0.110: 339 0.110 - 0.147: 32 0.147 - 0.183: 4 Chirality restraints: 4938 Sorted by residual: chirality pdb=" CB VAL N 155 " pdb=" CA VAL N 155 " pdb=" CG1 VAL N 155 " pdb=" CG2 VAL N 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CB VAL V 155 " pdb=" CA VAL V 155 " pdb=" CG1 VAL V 155 " pdb=" CG2 VAL V 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CB VAL L 155 " pdb=" CA VAL L 155 " pdb=" CG1 VAL L 155 " pdb=" CG2 VAL L 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 4935 not shown) Planarity restraints: 6129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 176 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C GLU A 176 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU A 176 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG A 177 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 176 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C GLU D 176 " 0.029 2.00e-02 2.50e+03 pdb=" O GLU D 176 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG D 177 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 70 " -0.006 2.00e-02 2.50e+03 1.12e-02 1.26e+00 pdb=" C GLN G 70 " 0.019 2.00e-02 2.50e+03 pdb=" O GLN G 70 " -0.007 2.00e-02 2.50e+03 pdb=" N ASN G 71 " -0.007 2.00e-02 2.50e+03 ... (remaining 6126 not shown) Histogram of nonbonded interaction distances: 0.98 - 1.77: 6 1.77 - 2.55: 447 2.55 - 3.33: 45791 3.33 - 4.12: 85400 4.12 - 4.90: 167935 Warning: very small nonbonded interaction distances. Nonbonded interactions: 299579 Sorted by model distance: nonbonded pdb="FE FE C 201 " pdb="FE FE F 201 " model vdw 0.983 1.480 nonbonded pdb="FE FE J 201 " pdb="FE FE Q 201 " model vdw 0.990 1.480 nonbonded pdb="FE FE I 201 " pdb="FE FE I 202 " model vdw 0.992 1.480 nonbonded pdb="FE FE S 201 " pdb="FE FE U 201 " model vdw 0.994 1.480 nonbonded pdb="FE FE O 201 " pdb="FE FE B 201 " model vdw 0.998 1.480 ... (remaining 299574 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 188) selection = (chain 'B' and resid 3 through 188) selection = (chain 'C' and resid 3 through 188) selection = (chain 'D' and resid 3 through 188) selection = chain 'E' selection = (chain 'F' and resid 3 through 188) selection = chain 'G' selection = (chain 'H' and resid 3 through 188) selection = (chain 'I' and resid 3 through 188) selection = (chain 'J' and resid 3 through 188) selection = chain 'K' selection = (chain 'L' and resid 3 through 188) selection = chain 'M' selection = (chain 'N' and resid 3 through 188) selection = (chain 'O' and resid 3 through 188) selection = chain 'P' selection = (chain 'Q' and resid 3 through 188) selection = (chain 'R' and resid 3 through 188) selection = (chain 'S' and resid 3 through 188) selection = chain 'T' selection = (chain 'U' and resid 3 through 188) selection = (chain 'V' and resid 3 through 188) selection = chain 'W' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 27.050 Find NCS groups from input model: 0.840 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 : 0.009 0.054 34359 Z= 0.386 Angle : 0.737 8.292 46146 Z= 0.413 Chirality : 0.040 0.183 4938 Planarity : 0.003 0.017 6129 Dihedral : 17.493 89.945 12882 Min Nonbonded Distance : 0.983 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 8.48 % Allowed : 19.03 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.11), residues: 4089 helix: -1.77 (0.07), residues: 3153 sheet: None (None), residues: 0 loop : -2.05 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 60 TYR 0.014 0.002 TYR D 173 PHE 0.013 0.002 PHE C 52 TRP 0.006 0.002 TRP R 90 HIS 0.010 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00865 (34359) covalent geometry : angle 0.73668 (46146) hydrogen bonds : bond 0.21081 ( 2600) hydrogen bonds : angle 7.63292 ( 7800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 300 poor density : 815 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8728 (t0) cc_final: 0.8439 (t0) REVERT: E 64 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7342 (tm-30) REVERT: E 81 ASP cc_start: 0.7553 (t0) cc_final: 0.7236 (t70) REVERT: E 108 ASN cc_start: 0.8695 (t0) cc_final: 0.8443 (t0) REVERT: G 22 ASN cc_start: 0.8482 (t0) cc_final: 0.8216 (t0) REVERT: H 108 ASN cc_start: 0.8752 (t0) cc_final: 0.8534 (t0) REVERT: H 145 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7824 (mtp) REVERT: I 145 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7612 (mtp) REVERT: J 108 ASN cc_start: 0.8748 (t0) cc_final: 0.8484 (t0) REVERT: K 108 ASN cc_start: 0.8789 (t0) cc_final: 0.8451 (t0) REVERT: L 108 ASN cc_start: 0.8762 (t0) cc_final: 0.8418 (t0) REVERT: M 108 ASN cc_start: 0.8770 (t0) cc_final: 0.8465 (t0) REVERT: M 144 LYS cc_start: 0.8840 (tptm) cc_final: 0.8546 (mtpp) REVERT: N 107 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8664 (tp) REVERT: N 108 ASN cc_start: 0.8731 (t0) cc_final: 0.8452 (t0) REVERT: N 144 LYS cc_start: 0.8911 (tptm) cc_final: 0.8534 (mtpp) REVERT: O 108 ASN cc_start: 0.8747 (t0) cc_final: 0.8483 (t0) REVERT: Q 108 ASN cc_start: 0.8750 (t0) cc_final: 0.8527 (t0) REVERT: Q 145 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7652 (mtp) REVERT: R 108 ASN cc_start: 0.8733 (t0) cc_final: 0.8418 (t0) REVERT: R 181 LYS cc_start: 0.8425 (tptt) cc_final: 0.8205 (tmtt) REVERT: S 108 ASN cc_start: 0.8701 (t0) cc_final: 0.8379 (t0) REVERT: T 105 LYS cc_start: 0.8402 (mtpt) cc_final: 0.8198 (mtpp) REVERT: V 108 ASN cc_start: 0.8720 (t0) cc_final: 0.8460 (t0) REVERT: B 108 ASN cc_start: 0.8655 (t0) cc_final: 0.8345 (t0) REVERT: D 64 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7220 (tm-30) REVERT: D 68 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6703 (mt-10) REVERT: D 108 ASN cc_start: 0.8762 (t0) cc_final: 0.8451 (t0) REVERT: F 64 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7503 (tm-30) REVERT: F 108 ASN cc_start: 0.8459 (t0) cc_final: 0.8193 (t0) outliers start: 300 outliers final: 246 residues processed: 1076 average time/residue: 0.2365 time to fit residues: 388.5471 Evaluate side-chains 952 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 702 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 42 ASP Chi-restraints excluded: chain Z residue 71 ASN Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 128 ASP Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain Z residue 139 VAL Chi-restraints excluded: chain Z residue 169 SER Chi-restraints excluded: chain Z residue 176 GLU Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 ASP Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 73 ARG Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 145 MET Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 71 ASN Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 127 CYS Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 14 GLU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 127 CYS Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 42 ASP Chi-restraints excluded: chain O residue 43 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 71 ASN Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 83 GLN Chi-restraints excluded: chain O residue 127 CYS Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 4 GLN Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 71 ASN Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 145 MET Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 41 ASP Chi-restraints excluded: chain R residue 42 ASP Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 71 ASN Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 71 ASN Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 145 MET Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain T residue 55 LEU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 71 ASN Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 145 MET Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 71 ASN Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 14 GLU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain V residue 43 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 127 CYS Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 43 VAL Chi-restraints excluded: chain W residue 55 LEU Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 89 GLU Chi-restraints excluded: chain W residue 132 SER Chi-restraints excluded: chain W residue 145 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 139 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 8 ASN Z 83 GLN Z 109 GLN Z 147 ASN ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 ASN A 83 GLN A 147 ASN A 148 HIS ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 83 GLN C 115 HIS C 147 ASN E 8 ASN E 70 GLN E 109 GLN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN G 8 ASN G 115 HIS G 147 ASN G 148 HIS H 8 ASN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN H 147 ASN I 8 ASN I 70 GLN I 83 GLN I 87 GLN I 108 ASN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN I 148 HIS J 8 ASN J 87 GLN ** J 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN J 182 HIS K 8 ASN K 22 ASN K 83 GLN ** K 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 ASN K 148 HIS ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN L 22 ASN L 87 GLN L 147 ASN L 148 HIS M 8 ASN M 22 ASN M 71 ASN M 83 GLN ** M 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 ASN M 148 HIS N 8 ASN N 22 ASN ** N 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 87 GLN N 109 GLN ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 ASN N 148 HIS O 8 ASN O 22 ASN O 87 GLN O 147 ASN O 148 HIS P 8 ASN P 22 ASN P 71 ASN P 83 GLN P 87 GLN P 115 HIS P 147 ASN ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN Q 83 GLN Q 87 GLN Q 147 ASN R 8 ASN R 87 GLN ** R 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 147 ASN S 8 ASN S 87 GLN S 147 ASN T 8 ASN T 87 GLN T 106 ASN T 108 ASN ** T 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 147 ASN U 8 ASN U 70 GLN U 87 GLN U 108 ASN U 147 ASN U 148 HIS V 8 ASN V 22 ASN V 70 GLN ** V 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN ** V 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 147 ASN W 8 ASN W 22 ASN W 71 ASN W 83 GLN ** W 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 147 ASN W 182 HIS ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 ASN B 83 GLN B 87 GLN B 115 HIS B 147 ASN D 8 ASN D 22 ASN D 83 GLN D 115 HIS D 133 HIS D 147 ASN D 148 HIS ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN F 22 ASN F 83 GLN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS F 147 ASN F 148 HIS Total number of N/Q/H flips: 118 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.133660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.123710 restraints weight = 57372.809| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.84 r_work: 0.3514 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34359 Z= 0.133 Angle : 0.548 8.245 46146 Z= 0.286 Chirality : 0.035 0.162 4938 Planarity : 0.004 0.028 6129 Dihedral : 10.088 79.929 5039 Min Nonbonded Distance : 1.262 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 5.48 % Allowed : 21.66 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.13), residues: 4089 helix: 1.17 (0.09), residues: 3258 sheet: None (None), residues: 0 loop : -1.53 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 121 TYR 0.012 0.002 TYR R 173 PHE 0.019 0.002 PHE F 129 TRP 0.006 0.001 TRP V 90 HIS 0.007 0.001 HIS O 115 Details of bonding type rmsd covalent geometry : bond 0.00295 (34359) covalent geometry : angle 0.54789 (46146) hydrogen bonds : bond 0.04016 ( 2600) hydrogen bonds : angle 4.18627 ( 7800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1338 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 1144 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 8 ASN cc_start: 0.9135 (OUTLIER) cc_final: 0.8832 (t0) REVERT: Z 64 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: Z 97 MET cc_start: 0.8342 (tpp) cc_final: 0.8131 (tpp) REVERT: Z 177 ARG cc_start: 0.8771 (tpp-160) cc_final: 0.8560 (mmp-170) REVERT: A 68 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7453 (mt-10) REVERT: A 92 LYS cc_start: 0.8045 (tppt) cc_final: 0.7669 (tppt) REVERT: A 108 ASN cc_start: 0.9025 (t0) cc_final: 0.8759 (t0) REVERT: A 181 LYS cc_start: 0.8531 (tptt) cc_final: 0.8237 (tmtt) REVERT: C 7 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8287 (pp30) REVERT: C 64 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8145 (tm-30) REVERT: C 97 MET cc_start: 0.8567 (tpp) cc_final: 0.8367 (tpp) REVERT: C 123 ASP cc_start: 0.8621 (t0) cc_final: 0.8409 (t0) REVERT: E 22 ASN cc_start: 0.8567 (t0) cc_final: 0.8346 (t0) REVERT: E 64 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8092 (tm-30) REVERT: E 104 GLU cc_start: 0.7476 (tp30) cc_final: 0.7102 (tp30) REVERT: E 121 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7653 (mtp-110) REVERT: G 97 MET cc_start: 0.8501 (tpp) cc_final: 0.8297 (tpp) REVERT: G 104 GLU cc_start: 0.7345 (tp30) cc_final: 0.6954 (tp30) REVERT: G 177 ARG cc_start: 0.8813 (tpp-160) cc_final: 0.8593 (mmp-170) REVERT: H 53 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.7975 (mtm-85) REVERT: H 108 ASN cc_start: 0.8964 (t0) cc_final: 0.8642 (t0) REVERT: H 121 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7858 (mtp-110) REVERT: I 53 ARG cc_start: 0.8217 (mtp-110) cc_final: 0.7770 (ttm170) REVERT: I 105 LYS cc_start: 0.8476 (mtpt) cc_final: 0.7979 (mttp) REVERT: I 121 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7653 (ttp80) REVERT: I 181 LYS cc_start: 0.8509 (tptt) cc_final: 0.8303 (tmtt) REVERT: J 6 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.7694 (ttm-80) REVERT: J 83 GLN cc_start: 0.8247 (tt0) cc_final: 0.7818 (tm-30) REVERT: J 108 ASN cc_start: 0.8970 (t0) cc_final: 0.8581 (t0) REVERT: J 181 LYS cc_start: 0.8795 (tmtt) cc_final: 0.8587 (tmtt) REVERT: K 105 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7782 (mtpp) REVERT: L 31 TYR cc_start: 0.9001 (m-80) cc_final: 0.8767 (m-80) REVERT: L 108 ASN cc_start: 0.8957 (t0) cc_final: 0.8654 (t0) REVERT: L 144 LYS cc_start: 0.8935 (tptm) cc_final: 0.8691 (mtpp) REVERT: L 181 LYS cc_start: 0.8539 (tptt) cc_final: 0.8210 (tmtt) REVERT: M 97 MET cc_start: 0.8416 (tpp) cc_final: 0.8186 (tpp) REVERT: M 108 ASN cc_start: 0.8963 (t0) cc_final: 0.8568 (t0) REVERT: N 108 ASN cc_start: 0.8966 (t0) cc_final: 0.8675 (t0) REVERT: N 134 TYR cc_start: 0.8664 (m-80) cc_final: 0.8368 (m-80) REVERT: O 97 MET cc_start: 0.8620 (tpp) cc_final: 0.8408 (tpp) REVERT: O 121 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7734 (ttp80) REVERT: P 104 GLU cc_start: 0.7402 (tp30) cc_final: 0.6952 (tp30) REVERT: P 138 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8259 (mm-30) REVERT: Q 53 ARG cc_start: 0.8193 (mtp-110) cc_final: 0.7846 (ttm170) REVERT: Q 105 LYS cc_start: 0.8424 (mtpt) cc_final: 0.8040 (mttp) REVERT: Q 138 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8266 (mm-30) REVERT: R 6 ARG cc_start: 0.8566 (ttt90) cc_final: 0.8356 (ttm-80) REVERT: R 104 GLU cc_start: 0.7188 (tp30) cc_final: 0.6884 (tp30) REVERT: R 108 ASN cc_start: 0.9040 (t0) cc_final: 0.8742 (t0) REVERT: S 59 LYS cc_start: 0.8860 (mmtp) cc_final: 0.8646 (mmtt) REVERT: S 108 ASN cc_start: 0.8974 (t0) cc_final: 0.8651 (t0) REVERT: S 178 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8882 (mt) REVERT: U 64 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7991 (tm-30) REVERT: U 105 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7839 (mtpp) REVERT: U 138 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8090 (mm-30) REVERT: V 105 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8088 (mtpp) REVERT: V 108 ASN cc_start: 0.9019 (t0) cc_final: 0.8787 (t0) REVERT: W 46 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7159 (mm-30) REVERT: W 138 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8067 (mm-30) REVERT: B 22 ASN cc_start: 0.8548 (t0) cc_final: 0.8343 (t0) REVERT: B 108 ASN cc_start: 0.8978 (t0) cc_final: 0.8722 (t0) REVERT: D 22 ASN cc_start: 0.8553 (t0) cc_final: 0.8334 (t0) REVERT: D 105 LYS cc_start: 0.8076 (mtpt) cc_final: 0.7748 (mmmt) REVERT: D 108 ASN cc_start: 0.9027 (t0) cc_final: 0.8704 (t0) REVERT: D 181 LYS cc_start: 0.8442 (tptt) cc_final: 0.8213 (tmtt) outliers start: 194 outliers final: 128 residues processed: 1301 average time/residue: 0.2245 time to fit residues: 451.2645 Evaluate side-chains 1030 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 894 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 8 ASN Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 83 GLN Chi-restraints excluded: chain Z residue 128 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 73 ARG Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 83 GLN Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain P residue 138 GLU Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain Q residue 138 GLU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 127 CYS Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 30 THR Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 138 GLU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 86 optimal weight: 1.9990 chunk 314 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 326 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 308 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 171 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 329 optimal weight: 0.9990 chunk 341 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 ASN ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 ASN ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 71 ASN E 8 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN H 8 ASN H 148 HIS I 8 ASN ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN I 108 ASN ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN ** J 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 HIS K 8 ASN ** K 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 71 ASN K 115 HIS ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 ASN L 83 GLN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN ** M 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 ASN M 115 HIS N 8 ASN ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 ASN ** O 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN O 108 ASN ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 108 ASN ** Q 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 ASN R 83 GLN ** R 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN S 83 GLN T 22 ASN T 108 ASN ** T 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 8 ASN ** U 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 71 ASN U 108 ASN V 8 ASN V 22 ASN V 71 ASN W 8 ASN ** W 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 71 ASN W 115 HIS W 182 HIS B 8 ASN D 8 ASN ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 ASN ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.132267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.121922 restraints weight = 57122.527| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.90 r_work: 0.3494 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34359 Z= 0.141 Angle : 0.537 8.162 46146 Z= 0.276 Chirality : 0.035 0.165 4938 Planarity : 0.003 0.048 6129 Dihedral : 8.519 85.160 4770 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 6.56 % Allowed : 23.24 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.13), residues: 4089 helix: 1.97 (0.09), residues: 3297 sheet: None (None), residues: 0 loop : -1.67 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 121 TYR 0.013 0.001 TYR P 31 PHE 0.016 0.002 PHE F 129 TRP 0.004 0.001 TRP V 90 HIS 0.005 0.001 HIS V 115 Details of bonding type rmsd covalent geometry : bond 0.00325 (34359) covalent geometry : angle 0.53739 (46146) hydrogen bonds : bond 0.03572 ( 2600) hydrogen bonds : angle 3.92997 ( 7800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 957 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 22 ASN cc_start: 0.8569 (t0) cc_final: 0.8367 (t0) REVERT: Z 64 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: Z 97 MET cc_start: 0.8134 (tpp) cc_final: 0.7925 (tpp) REVERT: Z 108 ASN cc_start: 0.9067 (t0) cc_final: 0.8717 (t0) REVERT: Z 177 ARG cc_start: 0.8775 (tpp-160) cc_final: 0.8551 (mmp-170) REVERT: A 89 GLU cc_start: 0.8562 (pp20) cc_final: 0.8297 (pp20) REVERT: A 121 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7778 (ttm-80) REVERT: A 181 LYS cc_start: 0.8519 (tptt) cc_final: 0.8251 (tmtt) REVERT: C 108 ASN cc_start: 0.9101 (t0) cc_final: 0.8836 (t0) REVERT: C 177 ARG cc_start: 0.8779 (tpp-160) cc_final: 0.8543 (mmm160) REVERT: E 22 ASN cc_start: 0.8564 (t0) cc_final: 0.8350 (t0) REVERT: E 83 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7542 (pp30) REVERT: E 121 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7594 (ttm-80) REVERT: E 138 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8336 (mm-30) REVERT: G 68 GLU cc_start: 0.8607 (tp30) cc_final: 0.8238 (pt0) REVERT: G 138 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8375 (mm-30) REVERT: G 177 ARG cc_start: 0.8827 (tpp-160) cc_final: 0.8601 (mmp-170) REVERT: H 97 MET cc_start: 0.8236 (tpp) cc_final: 0.8005 (tpp) REVERT: H 121 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7670 (ttm-80) REVERT: I 105 LYS cc_start: 0.8516 (mtpt) cc_final: 0.8143 (mtpp) REVERT: J 18 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8562 (m-40) REVERT: J 83 GLN cc_start: 0.8304 (tt0) cc_final: 0.7856 (tm-30) REVERT: J 89 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7797 (mm-30) REVERT: J 97 MET cc_start: 0.8249 (tpp) cc_final: 0.7963 (tpp) REVERT: J 108 ASN cc_start: 0.9069 (t0) cc_final: 0.8720 (t0) REVERT: K 80 GLN cc_start: 0.7603 (pt0) cc_final: 0.7340 (pt0) REVERT: K 105 LYS cc_start: 0.8218 (mtpt) cc_final: 0.7872 (mtpp) REVERT: L 31 TYR cc_start: 0.9044 (m-80) cc_final: 0.8750 (m-80) REVERT: L 76 ARG cc_start: 0.8884 (ttm170) cc_final: 0.8604 (ttm110) REVERT: L 104 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7316 (mm-30) REVERT: M 95 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7249 (tm-30) REVERT: M 97 MET cc_start: 0.8231 (tpp) cc_final: 0.7931 (tpp) REVERT: M 105 LYS cc_start: 0.8006 (mtpt) cc_final: 0.7663 (mtpp) REVERT: M 145 MET cc_start: 0.8520 (ttm) cc_final: 0.8312 (mtp) REVERT: N 105 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7991 (mttt) REVERT: O 121 ARG cc_start: 0.7853 (ttp80) cc_final: 0.7552 (ttp80) REVERT: O 145 MET cc_start: 0.8657 (ttm) cc_final: 0.8329 (mtp) REVERT: P 108 ASN cc_start: 0.9039 (t0) cc_final: 0.8762 (t0) REVERT: P 138 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8376 (mm-30) REVERT: Q 95 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7325 (tm-30) REVERT: Q 105 LYS cc_start: 0.8460 (mtpt) cc_final: 0.8063 (mttp) REVERT: R 22 ASN cc_start: 0.8467 (t0) cc_final: 0.8245 (t0) REVERT: R 60 ARG cc_start: 0.8314 (ttp80) cc_final: 0.7927 (ttp80) REVERT: R 89 GLU cc_start: 0.8608 (pp20) cc_final: 0.8316 (pm20) REVERT: R 104 GLU cc_start: 0.7070 (tp30) cc_final: 0.6798 (tp30) REVERT: S 22 ASN cc_start: 0.8610 (t0) cc_final: 0.8369 (t0) REVERT: S 178 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8879 (mt) REVERT: T 22 ASN cc_start: 0.8503 (t0) cc_final: 0.8299 (t0) REVERT: U 64 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7866 (tm-30) REVERT: U 68 GLU cc_start: 0.8416 (tp30) cc_final: 0.8128 (pt0) REVERT: U 105 LYS cc_start: 0.8351 (mtpt) cc_final: 0.8004 (mtpp) REVERT: V 83 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7719 (pt0) REVERT: V 97 MET cc_start: 0.8393 (tpp) cc_final: 0.8094 (tpp) REVERT: V 104 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7015 (mm-30) REVERT: V 105 LYS cc_start: 0.8396 (mtpt) cc_final: 0.8120 (mtpt) REVERT: W 97 MET cc_start: 0.7976 (tpp) cc_final: 0.7738 (tpp) REVERT: B 22 ASN cc_start: 0.8526 (t0) cc_final: 0.8310 (t0) REVERT: B 68 GLU cc_start: 0.8180 (tp30) cc_final: 0.7947 (tp30) REVERT: B 89 GLU cc_start: 0.8380 (pp20) cc_final: 0.8179 (pm20) REVERT: D 22 ASN cc_start: 0.8560 (t0) cc_final: 0.8359 (t0) REVERT: D 89 GLU cc_start: 0.8483 (pp20) cc_final: 0.8229 (pm20) REVERT: D 105 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7846 (mmmt) REVERT: D 181 LYS cc_start: 0.8509 (tptt) cc_final: 0.8130 (tmtt) outliers start: 232 outliers final: 165 residues processed: 1143 average time/residue: 0.2252 time to fit residues: 398.4634 Evaluate side-chains 1041 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 867 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 128 ASP Chi-restraints excluded: chain Z residue 145 MET Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 73 ARG Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 18 ASN Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain N residue 137 LYS Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 83 GLN Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain P residue 138 GLU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 145 MET Chi-restraints excluded: chain V residue 22 ASN Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 127 CYS Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 145 MET Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 39 ASP Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 186 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 384 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 295 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 205 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 ASN ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 ASN A 22 ASN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 71 ASN E 8 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS G 8 ASN G 71 ASN H 8 ASN H 71 ASN H 83 GLN ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 ASN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN J 115 HIS J 182 HIS K 8 ASN K 71 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN L 22 ASN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN M 71 ASN N 8 ASN N 22 ASN O 8 ASN ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN P 71 ASN ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 ASN R 115 HIS ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN T 108 ASN T 115 HIS U 8 ASN ** U 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 133 HIS V 8 ASN V 22 ASN W 8 ASN W 22 ASN W 71 ASN B 8 ASN B 71 ASN B 182 HIS D 8 ASN D 70 GLN ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN F 70 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.132702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122045 restraints weight = 56853.198| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.97 r_work: 0.3487 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34359 Z= 0.144 Angle : 0.532 8.114 46146 Z= 0.272 Chirality : 0.035 0.162 4938 Planarity : 0.003 0.041 6129 Dihedral : 8.069 87.086 4755 Min Nonbonded Distance : 1.248 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 6.64 % Allowed : 25.05 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.13), residues: 4089 helix: 2.30 (0.09), residues: 3321 sheet: None (None), residues: 0 loop : -1.78 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 53 TYR 0.015 0.001 TYR A 31 PHE 0.018 0.002 PHE V 69 TRP 0.003 0.001 TRP A 90 HIS 0.005 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00335 (34359) covalent geometry : angle 0.53192 (46146) hydrogen bonds : bond 0.03370 ( 2600) hydrogen bonds : angle 3.85348 ( 7800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 958 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 64 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: Z 97 MET cc_start: 0.8059 (tpp) cc_final: 0.7808 (tpp) REVERT: Z 108 ASN cc_start: 0.9058 (t0) cc_final: 0.8738 (t0) REVERT: Z 177 ARG cc_start: 0.8809 (tpp-160) cc_final: 0.8571 (mmp-170) REVERT: A 68 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7482 (mt-10) REVERT: A 89 GLU cc_start: 0.8565 (pp20) cc_final: 0.8338 (pp20) REVERT: A 105 LYS cc_start: 0.8373 (mtpt) cc_final: 0.7998 (mtpp) REVERT: A 181 LYS cc_start: 0.8556 (tptt) cc_final: 0.8245 (tmtt) REVERT: C 97 MET cc_start: 0.8080 (tpp) cc_final: 0.7848 (tpp) REVERT: C 105 LYS cc_start: 0.8432 (mtpt) cc_final: 0.8057 (mtpp) REVERT: C 108 ASN cc_start: 0.9148 (t0) cc_final: 0.8829 (t0) REVERT: C 177 ARG cc_start: 0.8856 (tpp-160) cc_final: 0.8585 (mmm160) REVERT: E 22 ASN cc_start: 0.8577 (t0) cc_final: 0.8376 (t0) REVERT: E 104 GLU cc_start: 0.7862 (tp30) cc_final: 0.7256 (tp30) REVERT: E 138 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8131 (mm-30) REVERT: G 108 ASN cc_start: 0.9150 (t0) cc_final: 0.8855 (t0) REVERT: G 138 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8292 (mm-30) REVERT: G 177 ARG cc_start: 0.8887 (tpp-160) cc_final: 0.8631 (mmp-170) REVERT: H 53 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.8126 (mtm-85) REVERT: H 68 GLU cc_start: 0.8450 (tp30) cc_final: 0.8244 (pt0) REVERT: H 97 MET cc_start: 0.8008 (tpp) cc_final: 0.7691 (tpp) REVERT: H 104 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7185 (mm-30) REVERT: H 105 LYS cc_start: 0.8352 (mtpt) cc_final: 0.7949 (mtpt) REVERT: I 105 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8145 (mtpt) REVERT: J 22 ASN cc_start: 0.8753 (t0) cc_final: 0.8545 (t0) REVERT: J 83 GLN cc_start: 0.8222 (tt0) cc_final: 0.7734 (tm-30) REVERT: J 89 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7717 (mm-30) REVERT: K 31 TYR cc_start: 0.9048 (m-80) cc_final: 0.8758 (m-80) REVERT: K 80 GLN cc_start: 0.7511 (pt0) cc_final: 0.7299 (pt0) REVERT: K 97 MET cc_start: 0.8154 (tpp) cc_final: 0.7903 (tpp) REVERT: K 104 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7741 (mm-30) REVERT: K 105 LYS cc_start: 0.8151 (mtpt) cc_final: 0.7797 (mtpp) REVERT: K 145 MET cc_start: 0.8638 (ttm) cc_final: 0.8407 (mtp) REVERT: L 76 ARG cc_start: 0.8952 (ttm170) cc_final: 0.8711 (ttm110) REVERT: L 97 MET cc_start: 0.8238 (tpp) cc_final: 0.8003 (tpp) REVERT: L 104 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7179 (mm-30) REVERT: M 31 TYR cc_start: 0.9055 (m-80) cc_final: 0.8749 (m-80) REVERT: M 80 GLN cc_start: 0.7530 (pt0) cc_final: 0.7296 (pt0) REVERT: M 95 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7410 (tm-30) REVERT: M 97 MET cc_start: 0.7950 (tpp) cc_final: 0.7681 (tpp) REVERT: M 105 LYS cc_start: 0.7997 (mtpt) cc_final: 0.7653 (mtpp) REVERT: N 68 GLU cc_start: 0.7728 (tp30) cc_final: 0.7401 (tp30) REVERT: O 97 MET cc_start: 0.8492 (tpp) cc_final: 0.8291 (tpp) REVERT: O 107 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8513 (mt) REVERT: O 121 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7580 (ttp80) REVERT: P 105 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8053 (mtpp) REVERT: P 108 ASN cc_start: 0.9096 (t0) cc_final: 0.8839 (t0) REVERT: P 138 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8134 (mm-30) REVERT: Q 105 LYS cc_start: 0.8467 (mtpt) cc_final: 0.8102 (mtpt) REVERT: R 60 ARG cc_start: 0.8276 (ttp80) cc_final: 0.7964 (tmm160) REVERT: R 89 GLU cc_start: 0.8615 (pp20) cc_final: 0.8299 (pm20) REVERT: S 22 ASN cc_start: 0.8579 (t0) cc_final: 0.8377 (t0) REVERT: S 178 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8833 (mt) REVERT: T 22 ASN cc_start: 0.8516 (t0) cc_final: 0.8294 (t0) REVERT: U 64 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8024 (tm-30) REVERT: U 105 LYS cc_start: 0.8387 (mtpt) cc_final: 0.7987 (mtpp) REVERT: U 108 ASN cc_start: 0.9088 (t0) cc_final: 0.8803 (t0) REVERT: V 83 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7617 (pt0) REVERT: V 97 MET cc_start: 0.7952 (tpp) cc_final: 0.7638 (tpp) REVERT: V 105 LYS cc_start: 0.8435 (mtpt) cc_final: 0.8110 (mtpt) REVERT: W 105 LYS cc_start: 0.8521 (mtpt) cc_final: 0.7997 (mtpp) REVERT: B 89 GLU cc_start: 0.8429 (pp20) cc_final: 0.8218 (pm20) REVERT: B 105 LYS cc_start: 0.8373 (mtpt) cc_final: 0.7910 (mtpp) REVERT: D 22 ASN cc_start: 0.8587 (t0) cc_final: 0.8384 (t0) REVERT: D 89 GLU cc_start: 0.8443 (pp20) cc_final: 0.8156 (pm20) REVERT: D 97 MET cc_start: 0.8382 (tpp) cc_final: 0.8116 (tpp) REVERT: D 104 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7189 (tp30) REVERT: D 181 LYS cc_start: 0.8453 (tptt) cc_final: 0.8092 (tmtt) REVERT: F 97 MET cc_start: 0.8238 (tpp) cc_final: 0.8026 (tpp) outliers start: 235 outliers final: 166 residues processed: 1144 average time/residue: 0.2244 time to fit residues: 396.5739 Evaluate side-chains 1050 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 876 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 128 ASP Chi-restraints excluded: chain Z residue 145 MET Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain N residue 137 LYS Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 83 GLN Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain P residue 138 GLU Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 145 MET Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 145 MET Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 39 ASP Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 323 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 327 optimal weight: 9.9990 chunk 312 optimal weight: 0.9990 chunk 345 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 371 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 403 optimal weight: 4.9990 chunk 358 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 8 ASN Z 22 ASN Z 83 GLN ** Z 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 ASN A 22 ASN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 71 ASN E 8 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS G 8 ASN H 8 ASN H 83 GLN ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 ASN I 71 ASN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN J 182 HIS K 71 ASN L 8 ASN L 22 ASN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN M 71 ASN N 8 ASN N 22 ASN ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 ASN ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN ** Q 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 ASN R 22 ASN R 83 GLN ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN T 108 ASN U 8 ASN U 22 ASN U 71 ASN ** U 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 ASN W 8 ASN W 22 ASN W 71 ASN W 182 HIS B 8 ASN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN F 8 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.133339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122390 restraints weight = 56487.731| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.97 r_work: 0.3464 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34359 Z= 0.128 Angle : 0.518 8.083 46146 Z= 0.266 Chirality : 0.035 0.158 4938 Planarity : 0.003 0.046 6129 Dihedral : 7.539 83.360 4744 Min Nonbonded Distance : 1.262 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 6.19 % Allowed : 25.93 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.13), residues: 4089 helix: 2.56 (0.09), residues: 3321 sheet: None (None), residues: 0 loop : -1.59 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 121 TYR 0.015 0.001 TYR A 31 PHE 0.013 0.002 PHE F 129 TRP 0.005 0.001 TRP F 90 HIS 0.006 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00297 (34359) covalent geometry : angle 0.51806 (46146) hydrogen bonds : bond 0.03179 ( 2600) hydrogen bonds : angle 3.79118 ( 7800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 977 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 97 MET cc_start: 0.8153 (tpp) cc_final: 0.7931 (tpp) REVERT: Z 108 ASN cc_start: 0.9098 (t0) cc_final: 0.8748 (t0) REVERT: A 68 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7339 (mt-10) REVERT: A 89 GLU cc_start: 0.8539 (pp20) cc_final: 0.8273 (pp20) REVERT: A 105 LYS cc_start: 0.8295 (mtpt) cc_final: 0.7960 (mtpp) REVERT: A 181 LYS cc_start: 0.8509 (tptt) cc_final: 0.8113 (tmtt) REVERT: C 83 GLN cc_start: 0.8235 (pt0) cc_final: 0.8033 (pt0) REVERT: C 105 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7944 (mtpt) REVERT: C 177 ARG cc_start: 0.8899 (tpp-160) cc_final: 0.8629 (mmm160) REVERT: E 104 GLU cc_start: 0.7934 (tp30) cc_final: 0.7217 (tp30) REVERT: E 108 ASN cc_start: 0.9101 (t0) cc_final: 0.8851 (t0) REVERT: E 138 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8378 (mm-30) REVERT: G 108 ASN cc_start: 0.9140 (t0) cc_final: 0.8859 (t0) REVERT: G 177 ARG cc_start: 0.8925 (tpp-160) cc_final: 0.8645 (mmp-170) REVERT: H 46 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7793 (mm-30) REVERT: H 105 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7821 (mttp) REVERT: I 68 GLU cc_start: 0.8389 (tp30) cc_final: 0.8140 (pt0) REVERT: I 104 GLU cc_start: 0.8050 (tp30) cc_final: 0.7447 (tp30) REVERT: I 108 ASN cc_start: 0.9113 (t0) cc_final: 0.8804 (t0) REVERT: J 22 ASN cc_start: 0.8634 (t0) cc_final: 0.8432 (t0) REVERT: J 83 GLN cc_start: 0.8223 (tt0) cc_final: 0.7727 (tm-30) REVERT: J 89 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7910 (mm-30) REVERT: K 31 TYR cc_start: 0.9069 (m-80) cc_final: 0.8662 (m-80) REVERT: K 80 GLN cc_start: 0.7432 (pt0) cc_final: 0.7225 (pt0) REVERT: L 31 TYR cc_start: 0.9098 (m-80) cc_final: 0.8752 (m-80) REVERT: L 76 ARG cc_start: 0.8848 (ttm170) cc_final: 0.8606 (ttm110) REVERT: L 97 MET cc_start: 0.8507 (tpp) cc_final: 0.8259 (tpp) REVERT: L 104 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7280 (mm-30) REVERT: M 31 TYR cc_start: 0.8977 (m-80) cc_final: 0.8656 (m-80) REVERT: M 68 GLU cc_start: 0.8268 (tp30) cc_final: 0.7976 (pt0) REVERT: M 95 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7620 (tm-30) REVERT: M 97 MET cc_start: 0.8122 (tpp) cc_final: 0.7886 (tpp) REVERT: N 105 LYS cc_start: 0.8370 (mtpp) cc_final: 0.8049 (mttt) REVERT: O 108 ASN cc_start: 0.9075 (t0) cc_final: 0.8690 (t0) REVERT: P 108 ASN cc_start: 0.9060 (t0) cc_final: 0.8811 (t0) REVERT: P 138 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8200 (mm-30) REVERT: Q 105 LYS cc_start: 0.8384 (mtpt) cc_final: 0.8007 (mtpt) REVERT: R 60 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8037 (tmm160) REVERT: R 68 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7242 (mp0) REVERT: R 89 GLU cc_start: 0.8555 (pp20) cc_final: 0.8241 (pm20) REVERT: R 105 LYS cc_start: 0.8412 (mtpt) cc_final: 0.7895 (mttp) REVERT: S 68 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7144 (mp0) REVERT: S 83 GLN cc_start: 0.8220 (pt0) cc_final: 0.7935 (pt0) REVERT: S 105 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7836 (mtpt) REVERT: S 178 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8772 (mt) REVERT: T 22 ASN cc_start: 0.8491 (t0) cc_final: 0.8260 (t0) REVERT: T 108 ASN cc_start: 0.8953 (t0) cc_final: 0.8650 (t0) REVERT: U 105 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7992 (mtpp) REVERT: U 108 ASN cc_start: 0.9141 (t0) cc_final: 0.8828 (t0) REVERT: U 138 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8242 (mm-30) REVERT: V 97 MET cc_start: 0.8333 (tpp) cc_final: 0.7970 (tpp) REVERT: V 108 ASN cc_start: 0.9111 (t0) cc_final: 0.8745 (t0) REVERT: W 97 MET cc_start: 0.7842 (tpp) cc_final: 0.7488 (tpp) REVERT: W 105 LYS cc_start: 0.8265 (mtpt) cc_final: 0.7819 (mtpp) REVERT: W 108 ASN cc_start: 0.9109 (t0) cc_final: 0.8748 (t0) REVERT: B 89 GLU cc_start: 0.8444 (pp20) cc_final: 0.8151 (pm20) REVERT: D 89 GLU cc_start: 0.8460 (pp20) cc_final: 0.8135 (pm20) REVERT: D 105 LYS cc_start: 0.8356 (mtpt) cc_final: 0.7928 (mtpt) REVERT: D 181 LYS cc_start: 0.8427 (tptt) cc_final: 0.8001 (tmtt) outliers start: 219 outliers final: 159 residues processed: 1144 average time/residue: 0.2239 time to fit residues: 398.4652 Evaluate side-chains 1051 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 887 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 83 GLN Chi-restraints excluded: chain Z residue 128 ASP Chi-restraints excluded: chain Z residue 145 MET Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain N residue 137 LYS Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 83 GLN Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain P residue 138 GLU Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 107 LEU Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 145 MET Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 3 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 204 optimal weight: 0.9980 chunk 376 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 266 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 171 optimal weight: 0.7980 chunk 326 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 22 ASN ** Z 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 ASN A 22 ASN A 70 GLN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 22 ASN E 8 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS G 8 ASN H 8 ASN H 83 GLN ** H 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 HIS I 8 ASN I 22 ASN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 HIS ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN K 8 ASN L 8 ASN M 8 ASN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 ASN ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN Q 8 ASN Q 22 ASN Q 71 ASN ** Q 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 ASN R 22 ASN R 83 GLN S 8 ASN S 22 ASN U 22 ASN ** U 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 ASN V 133 HIS W 8 ASN W 22 ASN W 182 HIS B 8 ASN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.134763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.123918 restraints weight = 56463.675| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.94 r_work: 0.3496 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34359 Z= 0.121 Angle : 0.520 8.103 46146 Z= 0.268 Chirality : 0.034 0.163 4938 Planarity : 0.003 0.047 6129 Dihedral : 6.972 82.570 4718 Min Nonbonded Distance : 1.276 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 6.14 % Allowed : 25.95 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.09 (0.14), residues: 4089 helix: 2.75 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : -1.31 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 121 TYR 0.015 0.001 TYR A 31 PHE 0.012 0.002 PHE V 69 TRP 0.004 0.000 TRP F 90 HIS 0.006 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00277 (34359) covalent geometry : angle 0.51996 (46146) hydrogen bonds : bond 0.03074 ( 2600) hydrogen bonds : angle 3.76203 ( 7800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 967 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 64 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: Z 121 ARG cc_start: 0.6982 (mtp-110) cc_final: 0.6566 (ttm-80) REVERT: A 68 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7394 (mt-10) REVERT: A 105 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7743 (mttp) REVERT: A 181 LYS cc_start: 0.8441 (tptt) cc_final: 0.8209 (tmtt) REVERT: C 83 GLN cc_start: 0.8246 (pt0) cc_final: 0.8043 (pt0) REVERT: C 105 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7970 (mtpt) REVERT: C 177 ARG cc_start: 0.8812 (tpp-160) cc_final: 0.8562 (mmm160) REVERT: E 71 ASN cc_start: 0.8791 (m-40) cc_final: 0.8449 (t0) REVERT: E 105 LYS cc_start: 0.8383 (mtpt) cc_final: 0.8048 (mtpp) REVERT: E 108 ASN cc_start: 0.9095 (t0) cc_final: 0.8837 (t0) REVERT: E 181 LYS cc_start: 0.8878 (tmtt) cc_final: 0.7913 (tppt) REVERT: E 182 HIS cc_start: 0.7123 (m90) cc_final: 0.6904 (m170) REVERT: G 105 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8060 (mtpp) REVERT: G 108 ASN cc_start: 0.9199 (t0) cc_final: 0.8915 (t0) REVERT: G 177 ARG cc_start: 0.8879 (tpp-160) cc_final: 0.8619 (mmp-170) REVERT: H 105 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7902 (mtpp) REVERT: H 108 ASN cc_start: 0.9074 (t0) cc_final: 0.8749 (t0) REVERT: I 53 ARG cc_start: 0.8483 (mmm-85) cc_final: 0.7839 (mtm-85) REVERT: I 108 ASN cc_start: 0.9104 (t0) cc_final: 0.8827 (t0) REVERT: J 83 GLN cc_start: 0.8234 (tt0) cc_final: 0.7807 (tm-30) REVERT: J 89 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: K 31 TYR cc_start: 0.8972 (m-80) cc_final: 0.8712 (m-80) REVERT: K 97 MET cc_start: 0.8134 (tpp) cc_final: 0.7930 (tpp) REVERT: K 103 MET cc_start: 0.8287 (tpp) cc_final: 0.8083 (tpp) REVERT: K 104 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7634 (mm-30) REVERT: K 105 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7744 (mtpp) REVERT: L 97 MET cc_start: 0.8302 (tpp) cc_final: 0.8001 (tpp) REVERT: L 181 LYS cc_start: 0.8788 (tmtt) cc_final: 0.7794 (tppt) REVERT: M 31 TYR cc_start: 0.8925 (m-80) cc_final: 0.8680 (m-80) REVERT: M 68 GLU cc_start: 0.8283 (tp30) cc_final: 0.7904 (tp30) REVERT: M 97 MET cc_start: 0.8034 (tpp) cc_final: 0.7817 (tpp) REVERT: N 68 GLU cc_start: 0.8317 (tp30) cc_final: 0.8083 (mt-10) REVERT: N 108 ASN cc_start: 0.9058 (t0) cc_final: 0.8725 (t0) REVERT: O 68 GLU cc_start: 0.8119 (tp30) cc_final: 0.7895 (pt0) REVERT: O 73 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7275 (mmt180) REVERT: O 83 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7651 (pt0) REVERT: O 108 ASN cc_start: 0.9076 (t0) cc_final: 0.8705 (t0) REVERT: O 121 ARG cc_start: 0.7472 (mtp-110) cc_final: 0.7258 (ttm-80) REVERT: P 105 LYS cc_start: 0.8406 (mtpt) cc_final: 0.8023 (mtpt) REVERT: P 108 ASN cc_start: 0.9073 (t0) cc_final: 0.8853 (t0) REVERT: R 68 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7296 (mp0) REVERT: R 89 GLU cc_start: 0.8478 (pp20) cc_final: 0.8203 (pm20) REVERT: R 105 LYS cc_start: 0.8433 (mtpt) cc_final: 0.7957 (mttp) REVERT: R 108 ASN cc_start: 0.9158 (t0) cc_final: 0.8800 (t0) REVERT: R 154 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7013 (ptp90) REVERT: S 68 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7219 (mp0) REVERT: S 83 GLN cc_start: 0.8125 (pt0) cc_final: 0.7904 (pt0) REVERT: T 68 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7249 (mp0) REVERT: T 105 LYS cc_start: 0.8363 (mtpt) cc_final: 0.7956 (mtpt) REVERT: T 108 ASN cc_start: 0.8960 (t0) cc_final: 0.8702 (t0) REVERT: U 64 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8020 (tm-30) REVERT: U 104 GLU cc_start: 0.7776 (tp30) cc_final: 0.6977 (tp30) REVERT: U 105 LYS cc_start: 0.8362 (mtpt) cc_final: 0.7989 (mtpt) REVERT: U 138 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: V 97 MET cc_start: 0.8295 (tpp) cc_final: 0.7963 (tpp) REVERT: V 108 ASN cc_start: 0.9103 (t0) cc_final: 0.8757 (t0) REVERT: W 105 LYS cc_start: 0.8336 (mtpt) cc_final: 0.7807 (mttp) REVERT: W 108 ASN cc_start: 0.9092 (t0) cc_final: 0.8741 (t0) REVERT: B 89 GLU cc_start: 0.8348 (pp20) cc_final: 0.8108 (pm20) REVERT: B 108 ASN cc_start: 0.9156 (t0) cc_final: 0.8791 (t0) REVERT: D 89 GLU cc_start: 0.8366 (pp20) cc_final: 0.8101 (pm20) REVERT: D 105 LYS cc_start: 0.8414 (mtpt) cc_final: 0.7981 (mtpp) REVERT: D 181 LYS cc_start: 0.8416 (tptt) cc_final: 0.8114 (tmtt) REVERT: F 64 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7493 (tm-30) REVERT: F 97 MET cc_start: 0.8015 (tpp) cc_final: 0.7811 (tpp) REVERT: F 104 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7587 (tp30) REVERT: F 108 ASN cc_start: 0.8996 (t0) cc_final: 0.8550 (t0) outliers start: 217 outliers final: 156 residues processed: 1123 average time/residue: 0.2237 time to fit residues: 389.5321 Evaluate side-chains 1064 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 902 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ASN Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 128 ASP Chi-restraints excluded: chain Z residue 145 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain N residue 137 LYS Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 83 GLN Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 22 ASN Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 154 ARG Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain U residue 145 MET Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 145 MET Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 95 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 343 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 324 optimal weight: 0.0770 chunk 312 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 ASN Z 22 ASN ** Z 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 148 HIS A 8 ASN A 22 ASN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 22 ASN E 8 ASN ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 HIS G 8 ASN H 8 ASN H 22 ASN H 83 GLN H 115 HIS I 8 ASN I 22 ASN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN J 22 ASN K 8 ASN L 8 ASN M 8 ASN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 ASN ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN P 148 HIS ** Q 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 ASN R 22 ASN R 83 GLN S 8 ASN S 22 ASN S 148 HIS ** T 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 ASN U 115 HIS V 8 ASN V 148 HIS W 8 ASN W 22 ASN W 148 HIS W 182 HIS ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 ASN B 80 GLN B 148 HIS ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN D 22 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.132622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121634 restraints weight = 56231.918| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.93 r_work: 0.3463 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 34359 Z= 0.159 Angle : 0.553 8.340 46146 Z= 0.283 Chirality : 0.036 0.158 4938 Planarity : 0.003 0.046 6129 Dihedral : 6.727 88.599 4692 Min Nonbonded Distance : 1.230 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 6.02 % Allowed : 26.86 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.14), residues: 4089 helix: 2.67 (0.09), residues: 3321 sheet: None (None), residues: 0 loop : -1.01 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 121 TYR 0.017 0.002 TYR A 31 PHE 0.011 0.002 PHE F 129 TRP 0.005 0.001 TRP K 90 HIS 0.007 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00370 (34359) covalent geometry : angle 0.55336 (46146) hydrogen bonds : bond 0.03300 ( 2600) hydrogen bonds : angle 3.81906 ( 7800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 904 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 64 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7461 (tt0) REVERT: Z 97 MET cc_start: 0.8202 (tpp) cc_final: 0.7856 (tpp) REVERT: Z 108 ASN cc_start: 0.9052 (t0) cc_final: 0.8752 (t0) REVERT: A 68 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7414 (mt-10) REVERT: A 105 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7815 (mtpt) REVERT: A 181 LYS cc_start: 0.8442 (tptt) cc_final: 0.8201 (tmtt) REVERT: C 177 ARG cc_start: 0.8895 (tpp-160) cc_final: 0.8620 (mmm160) REVERT: E 71 ASN cc_start: 0.8885 (t0) cc_final: 0.8506 (t0) REVERT: E 104 GLU cc_start: 0.7790 (tp30) cc_final: 0.7065 (tp30) REVERT: E 108 ASN cc_start: 0.9113 (t0) cc_final: 0.8868 (t0) REVERT: G 105 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8102 (mtpp) REVERT: G 108 ASN cc_start: 0.9176 (t0) cc_final: 0.8864 (t0) REVERT: H 105 LYS cc_start: 0.8297 (mtpt) cc_final: 0.7919 (mttp) REVERT: I 53 ARG cc_start: 0.8494 (mmm-85) cc_final: 0.7830 (mtm-85) REVERT: I 108 ASN cc_start: 0.9112 (t0) cc_final: 0.8800 (t0) REVERT: I 181 LYS cc_start: 0.8751 (tmtt) cc_final: 0.7777 (tppt) REVERT: J 83 GLN cc_start: 0.8196 (tt0) cc_final: 0.7763 (tm-30) REVERT: K 97 MET cc_start: 0.8285 (tpp) cc_final: 0.8030 (tpp) REVERT: K 105 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7753 (mtpp) REVERT: L 97 MET cc_start: 0.8508 (tpp) cc_final: 0.8203 (tpp) REVERT: L 104 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7324 (mm-30) REVERT: L 105 LYS cc_start: 0.8428 (mtpt) cc_final: 0.8007 (mtpp) REVERT: M 31 TYR cc_start: 0.8943 (m-80) cc_final: 0.8703 (m-80) REVERT: M 68 GLU cc_start: 0.8229 (tp30) cc_final: 0.8013 (tp30) REVERT: M 95 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7587 (tm-30) REVERT: M 97 MET cc_start: 0.8159 (tpp) cc_final: 0.7912 (tpp) REVERT: M 104 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7700 (mm-30) REVERT: M 105 LYS cc_start: 0.7975 (mtpt) cc_final: 0.7574 (mmmt) REVERT: N 68 GLU cc_start: 0.8284 (tp30) cc_final: 0.7984 (mt-10) REVERT: N 105 LYS cc_start: 0.8409 (mtpp) cc_final: 0.8053 (mttm) REVERT: O 83 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7673 (pt0) REVERT: O 104 GLU cc_start: 0.8076 (tp30) cc_final: 0.7391 (tp30) REVERT: O 108 ASN cc_start: 0.9074 (t0) cc_final: 0.8730 (t0) REVERT: O 138 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8317 (tp30) REVERT: P 105 LYS cc_start: 0.8422 (mtpt) cc_final: 0.7949 (mtpt) REVERT: P 108 ASN cc_start: 0.9098 (t0) cc_final: 0.8816 (t0) REVERT: R 68 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7191 (mp0) REVERT: R 89 GLU cc_start: 0.8562 (pp20) cc_final: 0.8249 (pm20) REVERT: R 105 LYS cc_start: 0.8460 (mtpt) cc_final: 0.7968 (mttp) REVERT: R 108 ASN cc_start: 0.9130 (t0) cc_final: 0.8780 (t0) REVERT: S 68 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7157 (mp0) REVERT: S 83 GLN cc_start: 0.8246 (pt0) cc_final: 0.7984 (pt0) REVERT: T 68 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7215 (mp0) REVERT: T 105 LYS cc_start: 0.8324 (mtpt) cc_final: 0.7850 (mtpt) REVERT: T 108 ASN cc_start: 0.8983 (t0) cc_final: 0.8708 (t0) REVERT: U 76 ARG cc_start: 0.8788 (ttm-80) cc_final: 0.8559 (ttm-80) REVERT: U 105 LYS cc_start: 0.8362 (mtpt) cc_final: 0.8010 (mtpt) REVERT: U 108 ASN cc_start: 0.9157 (t0) cc_final: 0.8850 (t0) REVERT: U 138 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8175 (mm-30) REVERT: V 97 MET cc_start: 0.8382 (tpp) cc_final: 0.8032 (tpp) REVERT: W 97 MET cc_start: 0.7965 (tpp) cc_final: 0.7743 (tpp) REVERT: W 105 LYS cc_start: 0.8397 (mtpt) cc_final: 0.7993 (mtpt) REVERT: W 108 ASN cc_start: 0.9092 (t0) cc_final: 0.8750 (t0) REVERT: B 89 GLU cc_start: 0.8396 (pp20) cc_final: 0.8130 (pm20) REVERT: B 108 ASN cc_start: 0.9166 (t0) cc_final: 0.8773 (t0) REVERT: D 68 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7192 (mt-10) REVERT: D 89 GLU cc_start: 0.8407 (pp20) cc_final: 0.8119 (pm20) REVERT: D 105 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8018 (mtpp) REVERT: D 181 LYS cc_start: 0.8541 (tptt) cc_final: 0.8139 (tmtt) REVERT: F 97 MET cc_start: 0.8256 (tpp) cc_final: 0.8015 (tpp) outliers start: 213 outliers final: 164 residues processed: 1059 average time/residue: 0.2199 time to fit residues: 361.6834 Evaluate side-chains 1025 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 857 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 145 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain N residue 137 LYS Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 83 GLN Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 22 ASN Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 145 MET Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 160 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 232 optimal weight: 8.9990 chunk 268 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 ASN Z 22 ASN Z 83 GLN ** Z 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 ASN A 22 ASN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 22 ASN E 8 ASN ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS G 8 ASN H 22 ASN H 83 GLN I 8 ASN I 22 ASN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN K 8 ASN K 83 GLN L 8 ASN M 8 ASN N 8 ASN ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN ** Q 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 22 ASN R 83 GLN ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN S 22 ASN T 22 ASN U 8 ASN U 22 ASN W 8 ASN W 182 HIS ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 ASN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.131814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120766 restraints weight = 56184.684| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.93 r_work: 0.3456 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34359 Z= 0.168 Angle : 0.567 8.038 46146 Z= 0.291 Chirality : 0.036 0.157 4938 Planarity : 0.003 0.053 6129 Dihedral : 6.491 82.242 4682 Min Nonbonded Distance : 1.220 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 5.82 % Allowed : 26.92 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.14), residues: 4089 helix: 2.65 (0.09), residues: 3321 sheet: None (None), residues: 0 loop : -1.01 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 121 TYR 0.019 0.002 TYR A 31 PHE 0.011 0.002 PHE V 36 TRP 0.006 0.001 TRP K 90 HIS 0.008 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00391 (34359) covalent geometry : angle 0.56735 (46146) hydrogen bonds : bond 0.03365 ( 2600) hydrogen bonds : angle 3.83721 ( 7800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 890 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 64 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: Z 97 MET cc_start: 0.8238 (tpp) cc_final: 0.8015 (tpp) REVERT: Z 108 ASN cc_start: 0.9032 (t0) cc_final: 0.8727 (t0) REVERT: Z 121 ARG cc_start: 0.7149 (mtp-110) cc_final: 0.6724 (ttm-80) REVERT: A 68 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7401 (mt-10) REVERT: A 105 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7868 (mtpt) REVERT: A 181 LYS cc_start: 0.8478 (tptt) cc_final: 0.8212 (tmtt) REVERT: C 105 LYS cc_start: 0.8418 (mtpt) cc_final: 0.7987 (mtpt) REVERT: C 177 ARG cc_start: 0.8934 (tpp-160) cc_final: 0.8710 (mmp-170) REVERT: E 71 ASN cc_start: 0.8871 (t0) cc_final: 0.8498 (t0) REVERT: E 105 LYS cc_start: 0.8378 (mtpt) cc_final: 0.8000 (mtpp) REVERT: E 108 ASN cc_start: 0.9146 (t0) cc_final: 0.8873 (t0) REVERT: E 181 LYS cc_start: 0.8916 (tmtt) cc_final: 0.7903 (tppt) REVERT: G 105 LYS cc_start: 0.8431 (mtpt) cc_final: 0.8063 (mtpp) REVERT: G 108 ASN cc_start: 0.9181 (t0) cc_final: 0.8883 (t0) REVERT: H 68 GLU cc_start: 0.8253 (tp30) cc_final: 0.7924 (mt-10) REVERT: H 105 LYS cc_start: 0.8359 (mtpt) cc_final: 0.7959 (mttp) REVERT: I 53 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.7757 (mtm-85) REVERT: I 108 ASN cc_start: 0.9142 (t0) cc_final: 0.8872 (t0) REVERT: J 68 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7390 (mp0) REVERT: J 83 GLN cc_start: 0.8253 (tt0) cc_final: 0.7805 (tm-30) REVERT: K 97 MET cc_start: 0.8329 (tpp) cc_final: 0.8049 (tpp) REVERT: L 105 LYS cc_start: 0.8418 (mtpt) cc_final: 0.7895 (mttp) REVERT: L 181 LYS cc_start: 0.8854 (tmtt) cc_final: 0.7758 (tppt) REVERT: M 31 TYR cc_start: 0.9011 (m-80) cc_final: 0.8769 (m-80) REVERT: M 68 GLU cc_start: 0.8231 (tp30) cc_final: 0.8011 (tp30) REVERT: M 95 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7587 (tm-30) REVERT: M 97 MET cc_start: 0.8253 (tpp) cc_final: 0.8013 (tpp) REVERT: M 105 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7765 (mtpp) REVERT: N 68 GLU cc_start: 0.8291 (tp30) cc_final: 0.7985 (mt-10) REVERT: N 83 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7739 (pt0) REVERT: N 105 LYS cc_start: 0.8369 (mtpp) cc_final: 0.8002 (mttp) REVERT: O 64 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7745 (tm-30) REVERT: O 83 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: O 104 GLU cc_start: 0.7996 (tp30) cc_final: 0.7351 (tp30) REVERT: O 108 ASN cc_start: 0.9066 (t0) cc_final: 0.8688 (t0) REVERT: O 138 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8264 (tp30) REVERT: P 105 LYS cc_start: 0.8389 (mtpt) cc_final: 0.7950 (mtpt) REVERT: P 108 ASN cc_start: 0.9084 (t0) cc_final: 0.8816 (t0) REVERT: R 68 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7243 (mp0) REVERT: R 89 GLU cc_start: 0.8571 (pp20) cc_final: 0.8257 (pm20) REVERT: R 108 ASN cc_start: 0.9132 (t0) cc_final: 0.8766 (t0) REVERT: R 154 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.7020 (ptp90) REVERT: S 68 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7187 (mp0) REVERT: S 83 GLN cc_start: 0.8236 (pt0) cc_final: 0.7954 (pt0) REVERT: T 68 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7221 (mp0) REVERT: T 108 ASN cc_start: 0.9017 (t0) cc_final: 0.8716 (t0) REVERT: U 64 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7979 (tm-30) REVERT: U 104 GLU cc_start: 0.7781 (tp30) cc_final: 0.7069 (tp30) REVERT: U 105 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8019 (mtpt) REVERT: U 108 ASN cc_start: 0.9146 (t0) cc_final: 0.8848 (t0) REVERT: U 138 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8116 (mm-30) REVERT: V 97 MET cc_start: 0.8395 (tpp) cc_final: 0.8035 (tpp) REVERT: W 97 MET cc_start: 0.7953 (tpp) cc_final: 0.7691 (tpp) REVERT: W 105 LYS cc_start: 0.8454 (mtpt) cc_final: 0.8013 (mtpt) REVERT: W 108 ASN cc_start: 0.9083 (t0) cc_final: 0.8758 (t0) REVERT: B 68 GLU cc_start: 0.7876 (tp30) cc_final: 0.7661 (tp30) REVERT: B 89 GLU cc_start: 0.8394 (pp20) cc_final: 0.8135 (pm20) REVERT: D 64 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7770 (tm-30) REVERT: D 68 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7267 (mt-10) REVERT: D 89 GLU cc_start: 0.8418 (pp20) cc_final: 0.8125 (pm20) REVERT: D 105 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8074 (mtpt) REVERT: D 181 LYS cc_start: 0.8441 (tptt) cc_final: 0.8170 (tmtt) REVERT: F 97 MET cc_start: 0.8210 (tpp) cc_final: 0.7989 (tpp) REVERT: F 105 LYS cc_start: 0.8364 (mtpt) cc_final: 0.8076 (mtpt) REVERT: F 108 ASN cc_start: 0.8990 (t0) cc_final: 0.8570 (t0) outliers start: 206 outliers final: 165 residues processed: 1038 average time/residue: 0.2185 time to fit residues: 352.4555 Evaluate side-chains 1030 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 859 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 83 GLN Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 145 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain N residue 137 LYS Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 83 GLN Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 107 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain R residue 22 ASN Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 154 ARG Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 22 ASN Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 128 ASP Chi-restraints excluded: chain V residue 145 MET Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 226 optimal weight: 3.9990 chunk 368 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 309 optimal weight: 4.9990 chunk 293 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 234 optimal weight: 0.3980 chunk 314 optimal weight: 5.9990 chunk 364 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 ASN Z 22 ASN Z 83 GLN ** Z 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 22 ASN C 148 HIS E 8 ASN ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS G 8 ASN G 83 GLN H 22 ASN H 83 GLN I 8 ASN I 22 ASN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN K 8 ASN K 83 GLN L 8 ASN M 8 ASN ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN ** Q 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 22 ASN R 83 GLN S 8 ASN S 22 ASN W 8 ASN ** W 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 182 HIS ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 ASN B 22 ASN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN D 22 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.135531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.124573 restraints weight = 56198.881| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.94 r_work: 0.3504 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34359 Z= 0.120 Angle : 0.545 8.082 46146 Z= 0.281 Chirality : 0.035 0.174 4938 Planarity : 0.003 0.059 6129 Dihedral : 6.209 83.900 4680 Min Nonbonded Distance : 1.292 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 4.83 % Allowed : 28.02 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.47 (0.14), residues: 4089 helix: 2.93 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : -0.75 (0.25), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 121 TYR 0.019 0.001 TYR C 31 PHE 0.012 0.001 PHE F 129 TRP 0.005 0.001 TRP A 90 HIS 0.008 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00276 (34359) covalent geometry : angle 0.54467 (46146) hydrogen bonds : bond 0.03030 ( 2600) hydrogen bonds : angle 3.75350 ( 7800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 955 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 31 TYR cc_start: 0.9293 (m-80) cc_final: 0.9092 (m-80) REVERT: Z 64 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: Z 108 ASN cc_start: 0.9087 (t0) cc_final: 0.8811 (t0) REVERT: A 68 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7423 (mt-10) REVERT: A 105 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7778 (mttp) REVERT: A 134 TYR cc_start: 0.8471 (m-80) cc_final: 0.8238 (m-80) REVERT: A 181 LYS cc_start: 0.8400 (tptt) cc_final: 0.8128 (tmtt) REVERT: C 64 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7530 (tm-30) REVERT: C 105 LYS cc_start: 0.8325 (mtpt) cc_final: 0.7908 (mtpt) REVERT: C 121 ARG cc_start: 0.7298 (ttp-170) cc_final: 0.6949 (ttp-170) REVERT: E 71 ASN cc_start: 0.8816 (t0) cc_final: 0.8469 (t0) REVERT: E 105 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7806 (mtpt) REVERT: E 108 ASN cc_start: 0.9148 (t0) cc_final: 0.8944 (t0) REVERT: G 105 LYS cc_start: 0.8330 (mtpt) cc_final: 0.7915 (mtpt) REVERT: G 108 ASN cc_start: 0.9161 (t0) cc_final: 0.8889 (t0) REVERT: H 68 GLU cc_start: 0.8216 (tp30) cc_final: 0.7984 (mt-10) REVERT: H 105 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7984 (mtpt) REVERT: I 53 ARG cc_start: 0.8411 (mmm-85) cc_final: 0.7768 (mtm-85) REVERT: I 68 GLU cc_start: 0.8320 (tp30) cc_final: 0.8113 (tp30) REVERT: I 108 ASN cc_start: 0.9117 (t0) cc_final: 0.8862 (t0) REVERT: J 68 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7390 (mp0) REVERT: J 83 GLN cc_start: 0.8161 (tt0) cc_final: 0.7764 (tm-30) REVERT: K 97 MET cc_start: 0.8196 (tpp) cc_final: 0.7935 (tpp) REVERT: K 105 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7764 (mttp) REVERT: L 181 LYS cc_start: 0.8794 (tmtt) cc_final: 0.7719 (tppt) REVERT: M 31 TYR cc_start: 0.8739 (m-80) cc_final: 0.8498 (m-80) REVERT: N 68 GLU cc_start: 0.8286 (tp30) cc_final: 0.8049 (mt-10) REVERT: N 83 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7554 (pt0) REVERT: N 105 LYS cc_start: 0.8348 (mtpp) cc_final: 0.8075 (mttt) REVERT: O 64 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7466 (tm-30) REVERT: O 104 GLU cc_start: 0.7897 (tp30) cc_final: 0.7131 (tp30) REVERT: O 108 ASN cc_start: 0.9077 (t0) cc_final: 0.8781 (t0) REVERT: O 121 ARG cc_start: 0.7473 (mtp-110) cc_final: 0.7124 (ttm-80) REVERT: O 138 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8182 (tp30) REVERT: P 105 LYS cc_start: 0.8317 (mtpt) cc_final: 0.7973 (mtpt) REVERT: P 108 ASN cc_start: 0.9094 (t0) cc_final: 0.8839 (t0) REVERT: R 68 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7283 (mp0) REVERT: R 89 GLU cc_start: 0.8492 (pp20) cc_final: 0.8228 (pm20) REVERT: R 154 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.7050 (ptp90) REVERT: S 68 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7267 (mp0) REVERT: S 83 GLN cc_start: 0.8158 (pt0) cc_final: 0.7894 (pt0) REVERT: T 68 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7223 (mp0) REVERT: T 105 LYS cc_start: 0.8378 (mtpt) cc_final: 0.8014 (mtpp) REVERT: T 108 ASN cc_start: 0.8992 (t0) cc_final: 0.8728 (t0) REVERT: U 64 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7879 (tm-30) REVERT: U 80 GLN cc_start: 0.7430 (pt0) cc_final: 0.7140 (mp10) REVERT: U 105 LYS cc_start: 0.8388 (mtpt) cc_final: 0.8037 (mtpt) REVERT: U 108 ASN cc_start: 0.9137 (t0) cc_final: 0.8908 (t0) REVERT: U 138 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8054 (mm-30) REVERT: V 97 MET cc_start: 0.8216 (tpp) cc_final: 0.7915 (tpp) REVERT: W 39 ASP cc_start: 0.7808 (t0) cc_final: 0.7577 (t70) REVERT: W 97 MET cc_start: 0.7883 (tpp) cc_final: 0.7634 (tpp) REVERT: W 105 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8081 (mtpp) REVERT: W 108 ASN cc_start: 0.9113 (t0) cc_final: 0.8799 (t0) REVERT: B 89 GLU cc_start: 0.8355 (pp20) cc_final: 0.8115 (pm20) REVERT: B 108 ASN cc_start: 0.9141 (t0) cc_final: 0.8832 (t0) REVERT: D 64 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7756 (tm-30) REVERT: D 68 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7301 (mt-10) REVERT: D 80 GLN cc_start: 0.7821 (pt0) cc_final: 0.7298 (mp10) REVERT: D 89 GLU cc_start: 0.8391 (pp20) cc_final: 0.8131 (pm20) REVERT: D 105 LYS cc_start: 0.8371 (mtpt) cc_final: 0.8055 (mtpt) REVERT: D 107 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8580 (mt) REVERT: D 181 LYS cc_start: 0.8481 (tptt) cc_final: 0.8210 (tmtt) REVERT: F 57 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6776 (mt-10) REVERT: F 105 LYS cc_start: 0.8310 (mtpt) cc_final: 0.8059 (mtpt) REVERT: F 108 ASN cc_start: 0.9000 (t0) cc_final: 0.8595 (t0) outliers start: 171 outliers final: 129 residues processed: 1077 average time/residue: 0.2189 time to fit residues: 365.9129 Evaluate side-chains 1031 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 896 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 145 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 128 ASP Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 83 GLN Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 128 ASP Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 154 ARG Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 268 optimal weight: 1.9990 chunk 302 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 144 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 344 optimal weight: 4.9990 chunk 301 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 ASN Z 22 ASN ** Z 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 HIS C 8 ASN C 22 ASN E 8 ASN ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS G 8 ASN G 83 GLN I 8 ASN I 22 ASN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN K 8 ASN L 8 ASN L 22 ASN M 8 ASN ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN Q 22 ASN ** Q 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN W 8 ASN ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 ASN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN F 8 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.133878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122655 restraints weight = 56664.375| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.00 r_work: 0.3475 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34359 Z= 0.148 Angle : 0.568 8.121 46146 Z= 0.293 Chirality : 0.036 0.155 4938 Planarity : 0.003 0.077 6129 Dihedral : 5.833 85.866 4661 Min Nonbonded Distance : 1.252 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 4.58 % Allowed : 28.72 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.28 (0.14), residues: 4089 helix: 2.83 (0.09), residues: 3327 sheet: None (None), residues: 0 loop : -1.04 (0.25), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 121 TYR 0.020 0.002 TYR P 31 PHE 0.012 0.002 PHE E 129 TRP 0.004 0.001 TRP V 90 HIS 0.008 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00345 (34359) covalent geometry : angle 0.56795 (46146) hydrogen bonds : bond 0.03224 ( 2600) hydrogen bonds : angle 3.83448 ( 7800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8178 Ramachandran restraints generated. 4089 Oldfield, 0 Emsley, 4089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 880 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 64 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: Z 108 ASN cc_start: 0.9053 (t0) cc_final: 0.8763 (t0) REVERT: Z 121 ARG cc_start: 0.7013 (mtp-110) cc_final: 0.6701 (ttm-80) REVERT: A 68 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7412 (mt-10) REVERT: A 105 LYS cc_start: 0.8259 (mtpt) cc_final: 0.7774 (mttp) REVERT: A 121 ARG cc_start: 0.7261 (mtp-110) cc_final: 0.6757 (ttm-80) REVERT: A 134 TYR cc_start: 0.8705 (m-80) cc_final: 0.8446 (m-80) REVERT: A 181 LYS cc_start: 0.8456 (tptt) cc_final: 0.8134 (tmtt) REVERT: C 105 LYS cc_start: 0.8326 (mtpt) cc_final: 0.7937 (mtpt) REVERT: C 121 ARG cc_start: 0.7439 (ttp-170) cc_final: 0.7021 (ttp-170) REVERT: E 71 ASN cc_start: 0.8803 (t0) cc_final: 0.8441 (t0) REVERT: E 105 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7885 (mtpt) REVERT: E 108 ASN cc_start: 0.9120 (t0) cc_final: 0.8848 (t0) REVERT: G 105 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7913 (mtpt) REVERT: H 68 GLU cc_start: 0.8335 (tp30) cc_final: 0.8125 (mt-10) REVERT: H 105 LYS cc_start: 0.8309 (mtpt) cc_final: 0.8012 (mtpt) REVERT: I 53 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.7777 (mtm-85) REVERT: I 68 GLU cc_start: 0.8300 (tp30) cc_final: 0.8098 (tp30) REVERT: I 108 ASN cc_start: 0.9109 (t0) cc_final: 0.8800 (t0) REVERT: J 68 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7378 (mp0) REVERT: J 83 GLN cc_start: 0.8238 (tt0) cc_final: 0.7762 (tm-30) REVERT: K 97 MET cc_start: 0.8227 (tpp) cc_final: 0.7925 (tpp) REVERT: K 105 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7797 (mttp) REVERT: L 105 LYS cc_start: 0.8446 (mtpt) cc_final: 0.7955 (mttp) REVERT: M 105 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7622 (mmtt) REVERT: N 68 GLU cc_start: 0.8285 (tp30) cc_final: 0.7984 (mt-10) REVERT: N 104 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7191 (mm-30) REVERT: N 105 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8147 (mttt) REVERT: O 64 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7487 (tm-30) REVERT: O 108 ASN cc_start: 0.9060 (t0) cc_final: 0.8739 (t0) REVERT: P 105 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7998 (mtpt) REVERT: P 108 ASN cc_start: 0.9092 (t0) cc_final: 0.8813 (t0) REVERT: R 68 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7210 (mp0) REVERT: R 89 GLU cc_start: 0.8500 (pp20) cc_final: 0.8192 (pm20) REVERT: R 108 ASN cc_start: 0.9118 (t0) cc_final: 0.8730 (t0) REVERT: R 154 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.6934 (ptp90) REVERT: S 68 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7236 (mp0) REVERT: S 83 GLN cc_start: 0.8227 (pt0) cc_final: 0.7922 (pt0) REVERT: T 22 ASN cc_start: 0.8639 (t0) cc_final: 0.8392 (t0) REVERT: T 68 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7158 (mp0) REVERT: U 64 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7957 (tm-30) REVERT: U 104 GLU cc_start: 0.7767 (tp30) cc_final: 0.6927 (tp30) REVERT: U 105 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8025 (mtpt) REVERT: U 138 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8146 (tp30) REVERT: V 97 MET cc_start: 0.8371 (tpp) cc_final: 0.7973 (tpp) REVERT: W 22 ASN cc_start: 0.8678 (t0) cc_final: 0.8474 (t0) REVERT: W 97 MET cc_start: 0.8073 (tpp) cc_final: 0.7804 (tpp) REVERT: W 108 ASN cc_start: 0.9096 (t0) cc_final: 0.8775 (t0) REVERT: B 89 GLU cc_start: 0.8408 (pp20) cc_final: 0.8121 (pm20) REVERT: D 89 GLU cc_start: 0.8454 (pp20) cc_final: 0.8152 (pm20) REVERT: D 105 LYS cc_start: 0.8404 (mtpt) cc_final: 0.8035 (mtpt) REVERT: D 181 LYS cc_start: 0.8503 (tptt) cc_final: 0.8166 (tmtt) REVERT: F 64 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7557 (tm-30) REVERT: F 105 LYS cc_start: 0.8350 (mtpt) cc_final: 0.8052 (mtpt) REVERT: F 108 ASN cc_start: 0.8984 (t0) cc_final: 0.8561 (t0) outliers start: 162 outliers final: 137 residues processed: 995 average time/residue: 0.2246 time to fit residues: 346.8190 Evaluate side-chains 1007 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 867 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 64 GLU Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain Z residue 107 LEU Chi-restraints excluded: chain Z residue 145 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 73 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 83 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 128 ASP Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 28 SER Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 128 ASP Chi-restraints excluded: chain Q residue 28 SER Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 154 ARG Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 128 ASP Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 55 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 78 LEU Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain V residue 145 MET Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 41 ASP Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 LEU Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 73 ARG Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 128 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 385 optimal weight: 0.0000 chunk 193 optimal weight: 0.6980 chunk 395 optimal weight: 3.9990 chunk 184 optimal weight: 0.0980 chunk 187 optimal weight: 6.9990 chunk 370 optimal weight: 0.9990 chunk 344 optimal weight: 3.9990 chunk 368 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 364 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 8 ASN Z 83 GLN ** Z 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS G 83 GLN H 83 GLN I 22 ASN ** I 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN K 8 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN M 8 ASN ** N 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN Q 22 ASN ** Q 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 22 ASN S 8 ASN S 22 ASN ** V 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 71 ASN W 8 ASN ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 ASN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN D 8 ASN F 8 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.137729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.126647 restraints weight = 56230.121| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.00 r_work: 0.3528 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34359 Z= 0.116 Angle : 0.548 8.048 46146 Z= 0.284 Chirality : 0.034 0.159 4938 Planarity : 0.003 0.074 6129 Dihedral : 5.498 86.823 4652 Min Nonbonded Distance : 1.315 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 4.04 % Allowed : 29.29 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.51 (0.14), residues: 4089 helix: 2.95 (0.09), residues: 3357 sheet: None (None), residues: 0 loop : -0.93 (0.26), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 121 TYR 0.021 0.001 TYR O 31 PHE 0.012 0.001 PHE H 36 TRP 0.004 0.000 TRP K 90 HIS 0.007 0.001 HIS L 115 Details of bonding type rmsd covalent geometry : bond 0.00262 (34359) covalent geometry : angle 0.54845 (46146) hydrogen bonds : bond 0.02976 ( 2600) hydrogen bonds : angle 3.74701 ( 7800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8946.79 seconds wall clock time: 153 minutes 58.87 seconds (9238.87 seconds total)