Starting phenix.real_space_refine on Wed Aug 5 17:57:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6puw_20483/08_2026/6puw_20483.cif Found real_map, /net/cci-nas-00/data/ceres_data/6puw_20483/08_2026/6puw_20483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6puw_20483/08_2026/6puw_20483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6puw_20483/08_2026/6puw_20483.map" model { file = "/net/cci-nas-00/data/ceres_data/6puw_20483/08_2026/6puw_20483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6puw_20483/08_2026/6puw_20483.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6puw_20483/08_2026/6puw_20483.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6puw_20483/08_2026/6puw_20483.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.024 sd= 0.693 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: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 72 5.49 5 Mg 4 5.21 5 S 34 5.16 5 C 6662 2.51 5 N 1914 2.21 5 O 2420 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11116 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1935 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "B" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 539 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "D" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} Chain: "E" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 371 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Conformer: "B" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} bond proxies already assigned to first conformer: 369 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "L" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 319 SG CYS A 40 26.812 44.982 52.090 1.00 27.12 S ATOM 342 SG CYS A 43 30.201 46.049 50.522 1.00 13.11 S ATOM 2241 SG CYS B 40 49.179 122.249 23.495 1.00 99.74 S ATOM 2264 SG CYS B 43 47.044 120.689 26.698 1.00107.94 S Restraints were copied for chains: G, H, I, J, K, L Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DA F 21 " occ=0.60 ... (40 atoms not shown) pdb=" C4 B DA F 21 " occ=0.40 residue: pdb=" P A DA L 21 " occ=0.60 ... (40 atoms not shown) pdb=" C4 B DA L 21 " occ=0.40 Time building chain proxies: 2.58, per 1000 atoms: 0.23 Number of scatterers: 11116 At special positions: 0 Unit cell: (92.43, 133.51, 83.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 34 16.00 P 72 15.00 Mg 4 11.99 F 6 9.00 O 2420 8.00 N 1914 7.00 C 6662 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: 1.05 Conformation dependent library (CDL) restraints added in 374.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 303 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 40 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 40 " pdb=" ZN G 303 " pdb="ZN ZN G 303 " - pdb=" NE2 HIS G 12 " pdb="ZN ZN G 303 " - pdb=" ND1 HIS G 16 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 43 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 40 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 12 " pdb="ZN ZN H 301 " - pdb=" ND1 HIS H 16 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 43 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 40 " Number of angles added : 4 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 14 sheets defined 47.2% alpha, 19.3% beta 30 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 removed outlier: 3.920A pdb=" N LYS A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 93 through 108 removed outlier: 3.598A pdb=" N TYR A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 166 Processing helix chain 'A' and resid 171 through 186 Processing helix chain 'A' and resid 195 through 221 removed outlier: 3.623A pdb=" N ILE A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 12 Processing helix chain 'B' and resid 18 through 27 removed outlier: 3.563A pdb=" N SER B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 39 Processing helix chain 'B' and resid 93 through 108 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 150 through 166 Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 171 through 186 Processing helix chain 'B' and resid 196 through 220 removed outlier: 3.602A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 222 Processing helix chain 'C' and resid 270 through 275 removed outlier: 3.735A pdb=" N GLN C 274 " --> pdb=" O TYR C 271 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET C 275 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 16 removed outlier: 3.920A pdb=" N LYS G 14 " --> pdb=" O GLU G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 26 Processing helix chain 'G' and resid 29 through 39 Processing helix chain 'G' and resid 40 through 44 Processing helix chain 'G' and resid 93 through 108 removed outlier: 3.598A pdb=" N TYR G 99 " --> pdb=" O GLN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 123 Processing helix chain 'G' and resid 123 through 134 Processing helix chain 'G' and resid 144 through 147 Processing helix chain 'G' and resid 148 through 166 Processing helix chain 'G' and resid 171 through 186 Processing helix chain 'G' and resid 195 through 221 removed outlier: 3.623A pdb=" N ILE G 220 " --> pdb=" O GLN G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 12 Processing helix chain 'H' and resid 18 through 27 removed outlier: 3.563A pdb=" N SER H 24 " --> pdb=" O ARG H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 39 Processing helix chain 'H' and resid 93 through 108 Processing helix chain 'H' and resid 123 through 134 Processing helix chain 'H' and resid 150 through 166 Processing helix chain 'H' and resid 167 through 169 No H-bonds generated for 'chain 'H' and resid 167 through 169' Processing helix chain 'H' and resid 171 through 186 Processing helix chain 'H' and resid 196 through 220 removed outlier: 3.602A pdb=" N ILE H 220 " --> pdb=" O GLN H 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 222 Processing helix chain 'I' and resid 270 through 275 removed outlier: 3.735A pdb=" N GLN I 274 " --> pdb=" O TYR I 271 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET I 275 " --> pdb=" O GLY I 272 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.251A pdb=" N VAL A 72 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP A 61 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL A 113 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.623A pdb=" N TRP A 243 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 84 through 89 removed outlier: 4.086A pdb=" N VAL B 72 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL B 113 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 188 through 189 Processing sheet with id=5, first strand: chain 'B' and resid 240 through 244 removed outlier: 5.751A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP B 243 " --> pdb=" O VAL B 250 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'C' and resid 256 through 261 removed outlier: 7.091A pdb=" N ALA C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS C 244 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 250 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 256 through 261 removed outlier: 6.527A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL D 225 " --> pdb=" O PRO D 238 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG D 224 " --> pdb=" O ILE D 268 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'G' and resid 87 through 89 removed outlier: 4.251A pdb=" N VAL G 72 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP G 61 " --> pdb=" O HIS G 114 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL G 113 " --> pdb=" O GLU G 138 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'G' and resid 224 through 225 removed outlier: 3.623A pdb=" N TRP G 243 " --> pdb=" O VAL G 250 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'H' and resid 84 through 89 removed outlier: 4.086A pdb=" N VAL H 72 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL H 113 " --> pdb=" O GLU H 138 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'H' and resid 188 through 189 Processing sheet with id=12, first strand: chain 'H' and resid 240 through 244 removed outlier: 5.751A pdb=" N LEU H 241 " --> pdb=" O GLN H 252 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN H 252 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP H 243 " --> pdb=" O VAL H 250 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'I' and resid 256 through 261 removed outlier: 7.091A pdb=" N ALA I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS I 244 " --> pdb=" O ALA I 248 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL I 250 " --> pdb=" O LEU I 242 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'J' and resid 256 through 261 removed outlier: 6.527A pdb=" N GLN J 252 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU J 241 " --> pdb=" O GLN J 252 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL J 225 " --> pdb=" O PRO J 238 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG J 224 " --> pdb=" O ILE J 268 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1632 1.31 - 1.43: 3202 1.43 - 1.56: 6130 1.56 - 1.68: 146 1.68 - 1.81: 50 Bond restraints: 11160 Sorted by residual: bond pdb=" CAN KLQ A 304 " pdb=" CBB KLQ A 304 " ideal model delta sigma weight residual 1.520 1.276 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" CAN KLQ G 304 " pdb=" CBB KLQ G 304 " ideal model delta sigma weight residual 1.520 1.276 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" CBD KLQ G 304 " pdb=" OAQ KLQ G 304 " ideal model delta sigma weight residual 1.390 1.625 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" CBD KLQ A 304 " pdb=" OAQ KLQ A 304 " ideal model delta sigma weight residual 1.390 1.625 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" O3' DC F 20 " pdb=" P B DA F 21 " ideal model delta sigma weight residual 1.607 1.485 0.122 1.20e-02 6.94e+03 1.04e+02 ... (remaining 11155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 15136 2.38 - 4.76: 208 4.76 - 7.14: 28 7.14 - 9.52: 0 9.52 - 11.90: 2 Bond angle restraints: 15374 Sorted by residual: angle pdb=" N SER G 123 " pdb=" CA SER G 123 " pdb=" C SER G 123 " ideal model delta sigma weight residual 110.41 117.17 -6.76 1.23e+00 6.61e-01 3.02e+01 angle pdb=" N SER A 123 " pdb=" CA SER A 123 " pdb=" C SER A 123 " ideal model delta sigma weight residual 110.41 117.17 -6.76 1.23e+00 6.61e-01 3.02e+01 angle pdb=" O LYS G 127 " pdb=" C LYS G 127 " pdb=" N ALA G 128 " ideal model delta sigma weight residual 122.15 116.92 5.23 1.14e+00 7.69e-01 2.10e+01 angle pdb=" O LYS A 127 " pdb=" C LYS A 127 " pdb=" N ALA A 128 " ideal model delta sigma weight residual 122.15 116.92 5.23 1.14e+00 7.69e-01 2.10e+01 angle pdb=" N3 DT L 17 " pdb=" C4 DT L 17 " pdb=" O4 DT L 17 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 ... (remaining 15369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 5490 17.33 - 34.67: 594 34.67 - 52.00: 310 52.00 - 69.33: 152 69.33 - 86.66: 16 Dihedral angle restraints: 6562 sinusoidal: 3224 harmonic: 3338 Sorted by residual: dihedral pdb=" CA ARG D 228 " pdb=" C ARG D 228 " pdb=" N ASP D 229 " pdb=" CA ASP D 229 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ARG J 228 " pdb=" C ARG J 228 " pdb=" N ASP J 229 " pdb=" CA ASP J 229 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA TYR G 194 " pdb=" C TYR G 194 " pdb=" N SER G 195 " pdb=" CA SER G 195 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 6559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1472 0.067 - 0.134: 218 0.134 - 0.201: 12 0.201 - 0.268: 4 0.268 - 0.336: 2 Chirality restraints: 1708 Sorted by residual: chirality pdb=" CBC KLQ A 304 " pdb=" CAM KLQ A 304 " pdb=" CAN KLQ A 304 " pdb=" NBE KLQ A 304 " both_signs ideal model delta sigma weight residual False -2.86 -2.53 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CBC KLQ G 304 " pdb=" CAM KLQ G 304 " pdb=" CAN KLQ G 304 " pdb=" NBE KLQ G 304 " both_signs ideal model delta sigma weight residual False -2.86 -2.53 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CBD KLQ G 304 " pdb=" CAO KLQ G 304 " pdb=" NBE KLQ G 304 " pdb=" OAQ KLQ G 304 " both_signs ideal model delta sigma weight residual False 2.41 2.66 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1705 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 127 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C LYS G 127 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS G 127 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA G 128 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 127 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C LYS A 127 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS A 127 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 128 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 155 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" C ASN G 155 " 0.022 2.00e-02 2.50e+03 pdb=" O ASN G 155 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS G 156 " -0.007 2.00e-02 2.50e+03 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 8 0.98 - 1.96: 8 1.96 - 2.94: 4699 2.94 - 3.92: 30716 3.92 - 4.90: 60476 Warning: very small nonbonded interaction distances. Nonbonded interactions: 95907 Sorted by model distance: nonbonded pdb=" O HOH A 464 " pdb=" O HOH G 438 " model vdw 0.000 3.040 nonbonded pdb=" O HOH A 459 " pdb=" O HOH L 109 " model vdw 0.000 3.040 nonbonded pdb=" O HOH A 488 " pdb=" O HOH K 105 " model vdw 0.000 3.040 nonbonded pdb=" O HOH E 105 " pdb=" O HOH G 488 " model vdw 0.000 3.040 nonbonded pdb=" O HOH F 109 " pdb=" O HOH G 459 " model vdw 0.000 3.040 ... (remaining 95902 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'L' } 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=0.40 max=1.00 mean=1.00 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: 4.920 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.280 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 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 0.244 11176 Z= 0.522 Angle : 0.709 13.487 15378 Z= 0.479 Chirality : 0.049 0.336 1708 Planarity : 0.003 0.026 1676 Dihedral : 19.820 86.664 4402 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.20 % Allowed : 2.66 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.24 (0.21), residues: 1130 helix: -1.14 (0.20), residues: 494 sheet: -1.04 (0.35), residues: 192 loop : -1.93 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 224 TYR 0.009 0.001 TYR A 194 PHE 0.008 0.001 PHE G 185 TRP 0.009 0.001 TRP H 19 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00888 / 0.52 (11160) covalent geometry : angle 0.69239 / 0.48 (15374) hydrogen bonds : bond 0.14024 / 9.62 ( 576) hydrogen bonds : angle 6.65583 / 4.67 ( 1568) metal coordination : bond 0.08287 / 4.84 ( 16) metal coordination : angle 9.59377 / 7.85 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 0.419 Fit side-chains TARDY: cannot create tardy model for: "GLU A 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 20 ARG cc_start: 0.8833 (ttm-80) cc_final: 0.8038 (ttp-170) REVERT: A 154 MET cc_start: 0.9280 (mmt) cc_final: 0.8885 (mmt) REVERT: B 35 GLU cc_start: 0.8053 (tp30) cc_final: 0.7266 (mp0) REVERT: B 251 ILE cc_start: 0.8842 (mm) cc_final: 0.8502 (pp) REVERT: G 20 ARG cc_start: 0.8832 (ttm-80) cc_final: 0.8039 (ttp-170) REVERT: G 154 MET cc_start: 0.9281 (mmt) cc_final: 0.8885 (mmt) REVERT: H 35 GLU cc_start: 0.8049 (tp30) cc_final: 0.7266 (mp0) REVERT: H 251 ILE cc_start: 0.8845 (mm) cc_final: 0.8503 (pp) outliers start: 2 outliers final: 2 residues processed: 220 average time/residue: 0.6547 time to fit residues: 153.8792 Evaluate side-chains 162 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain G residue 120 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 GLN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN C 221 GLN G 168 GLN ** H 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN I 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.094765 restraints weight = 14124.551| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.68 r_work: 0.2847 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11176 Z= 0.212 Angle : 0.558 5.348 15378 Z= 0.314 Chirality : 0.045 0.157 1708 Planarity : 0.004 0.028 1676 Dihedral : 22.089 60.420 2150 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.45 % Allowed : 11.04 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.02 (0.23), residues: 1130 helix: 0.29 (0.22), residues: 498 sheet: -0.89 (0.34), residues: 192 loop : -1.62 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 263 TYR 0.012 0.002 TYR G 194 PHE 0.009 0.001 PHE A 185 TRP 0.009 0.001 TRP H 132 HIS 0.011 0.002 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (11160) covalent geometry : angle 0.55701 / 0.31 (15374) hydrogen bonds : bond 0.04284 / 2.86 ( 576) hydrogen bonds : angle 4.96020 / 3.52 ( 1568) metal coordination : bond 0.00995 / 0.55 ( 16) metal coordination : angle 1.84204 / 1.44 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.397 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 20 ARG cc_start: 0.8814 (ttm-80) cc_final: 0.8000 (ttp-170) REVERT: A 136 LYS cc_start: 0.8595 (tttm) cc_final: 0.8343 (tptp) REVERT: B 35 GLU cc_start: 0.8113 (tp30) cc_final: 0.6984 (mp0) REVERT: B 251 ILE cc_start: 0.8888 (mm) cc_final: 0.8545 (pp) REVERT: B 258 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7669 (ttmm) REVERT: G 20 ARG cc_start: 0.8812 (ttm-80) cc_final: 0.7997 (ttp-170) REVERT: G 136 LYS cc_start: 0.8598 (tttm) cc_final: 0.8343 (tptp) REVERT: H 35 GLU cc_start: 0.8109 (tp30) cc_final: 0.6977 (mp0) REVERT: H 251 ILE cc_start: 0.8888 (mm) cc_final: 0.8549 (pp) REVERT: H 258 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7649 (ttmm) outliers start: 24 outliers final: 6 residues processed: 170 average time/residue: 0.5824 time to fit residues: 106.5306 Evaluate side-chains 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 51 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS A 148 GLN B 117 ASN C 221 GLN ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN I 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.132350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.095875 restraints weight = 18146.420| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.94 r_work: 0.2867 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11176 Z= 0.142 Angle : 0.502 5.626 15378 Z= 0.286 Chirality : 0.043 0.151 1708 Planarity : 0.003 0.027 1676 Dihedral : 21.978 60.326 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.25 % Allowed : 12.07 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.23), residues: 1130 helix: 1.00 (0.22), residues: 500 sheet: -0.66 (0.33), residues: 194 loop : -1.47 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 20 TYR 0.011 0.001 TYR A 194 PHE 0.007 0.001 PHE G 185 TRP 0.008 0.001 TRP B 132 HIS 0.009 0.001 HIS H 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (11160) covalent geometry : angle 0.50191 / 0.29 (15374) hydrogen bonds : bond 0.03679 / 2.45 ( 576) hydrogen bonds : angle 4.63080 / 3.30 ( 1568) metal coordination : bond 0.00407 / 0.25 ( 16) metal coordination : angle 0.77306 / 0.62 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.393 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 20 ARG cc_start: 0.8828 (ttm-80) cc_final: 0.8026 (ttp-170) REVERT: A 136 LYS cc_start: 0.8642 (tttm) cc_final: 0.8406 (tptp) REVERT: B 35 GLU cc_start: 0.8042 (tp30) cc_final: 0.6919 (mp0) REVERT: B 258 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7727 (mtmt) REVERT: G 20 ARG cc_start: 0.8822 (ttm-80) cc_final: 0.8023 (ttp-170) REVERT: G 136 LYS cc_start: 0.8645 (tttm) cc_final: 0.8407 (tptp) REVERT: H 35 GLU cc_start: 0.8045 (tp30) cc_final: 0.6917 (mp0) REVERT: H 258 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7722 (mtmt) outliers start: 22 outliers final: 4 residues processed: 178 average time/residue: 0.5800 time to fit residues: 111.2506 Evaluate side-chains 160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 19 optimal weight: 0.0870 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 0.0030 overall best weight: 0.7572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN B 117 ASN C 221 GLN ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS G 148 GLN G 155 ASN H 117 ASN I 221 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.095673 restraints weight = 15802.308| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.82 r_work: 0.2853 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11176 Z= 0.137 Angle : 0.487 5.199 15378 Z= 0.277 Chirality : 0.042 0.145 1708 Planarity : 0.003 0.027 1676 Dihedral : 21.869 60.650 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.25 % Allowed : 13.91 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.02 (0.24), residues: 1130 helix: 1.31 (0.22), residues: 500 sheet: -0.46 (0.34), residues: 194 loop : -1.28 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 224 TYR 0.010 0.001 TYR A 194 PHE 0.013 0.001 PHE H 26 TRP 0.008 0.001 TRP H 132 HIS 0.004 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (11160) covalent geometry : angle 0.48726 / 0.28 (15374) hydrogen bonds : bond 0.03470 / 2.31 ( 576) hydrogen bonds : angle 4.46788 / 3.19 ( 1568) metal coordination : bond 0.00515 / 0.31 ( 16) metal coordination : angle 0.88815 / 0.69 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.365 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 20 ARG cc_start: 0.8793 (ttm-80) cc_final: 0.7969 (ttp-170) REVERT: A 95 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: A 136 LYS cc_start: 0.8641 (tttm) cc_final: 0.8387 (tptp) REVERT: B 35 GLU cc_start: 0.7983 (tp30) cc_final: 0.6792 (mp0) REVERT: G 20 ARG cc_start: 0.8783 (ttm-80) cc_final: 0.7963 (ttp-170) REVERT: G 95 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: H 35 GLU cc_start: 0.7974 (tp30) cc_final: 0.6784 (mp0) outliers start: 22 outliers final: 10 residues processed: 171 average time/residue: 0.6012 time to fit residues: 110.8332 Evaluate side-chains 164 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 95 GLN Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 260 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN B 117 ASN G 155 ASN H 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.095145 restraints weight = 17972.886| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.95 r_work: 0.2839 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11176 Z= 0.156 Angle : 0.489 5.130 15378 Z= 0.277 Chirality : 0.043 0.145 1708 Planarity : 0.003 0.027 1676 Dihedral : 21.912 60.801 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.45 % Allowed : 15.13 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.19 (0.24), residues: 1130 helix: 1.43 (0.22), residues: 500 sheet: -0.33 (0.34), residues: 194 loop : -1.19 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 224 TYR 0.011 0.001 TYR A 194 PHE 0.008 0.001 PHE A 185 TRP 0.009 0.001 TRP B 131 HIS 0.003 0.001 HIS G 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (11160) covalent geometry : angle 0.48914 / 0.28 (15374) hydrogen bonds : bond 0.03466 / 2.31 ( 576) hydrogen bonds : angle 4.43924 / 3.17 ( 1568) metal coordination : bond 0.00557 / 0.35 ( 16) metal coordination : angle 1.01872 / 0.79 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.443 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 20 ARG cc_start: 0.8834 (ttm-80) cc_final: 0.8038 (ttp-170) REVERT: A 136 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8410 (tptp) REVERT: B 35 GLU cc_start: 0.8041 (tp30) cc_final: 0.6816 (mp0) REVERT: G 20 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8032 (ttp-170) REVERT: G 136 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8397 (tptp) REVERT: H 35 GLU cc_start: 0.8037 (tp30) cc_final: 0.6809 (mp0) outliers start: 24 outliers final: 8 residues processed: 164 average time/residue: 0.6519 time to fit residues: 114.9244 Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 136 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 260 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 91 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN B 117 ASN G 155 ASN H 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.099519 restraints weight = 19096.510| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.98 r_work: 0.2860 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11176 Z= 0.129 Angle : 0.476 5.303 15378 Z= 0.270 Chirality : 0.042 0.146 1708 Planarity : 0.003 0.027 1676 Dihedral : 21.894 60.694 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.25 % Allowed : 15.95 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1130 helix: 1.61 (0.22), residues: 498 sheet: -0.17 (0.35), residues: 194 loop : -1.12 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 199 TYR 0.009 0.001 TYR B 83 PHE 0.008 0.001 PHE B 26 TRP 0.010 0.001 TRP H 131 HIS 0.002 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (11160) covalent geometry : angle 0.47618 / 0.27 (15374) hydrogen bonds : bond 0.03282 / 2.19 ( 576) hydrogen bonds : angle 4.36614 / 3.11 ( 1568) metal coordination : bond 0.00373 / 0.22 ( 16) metal coordination : angle 0.72849 / 0.59 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.413 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 20 ARG cc_start: 0.8801 (ttm-80) cc_final: 0.7987 (ttp-170) REVERT: B 35 GLU cc_start: 0.7958 (tp30) cc_final: 0.6764 (mp0) REVERT: G 20 ARG cc_start: 0.8796 (ttm-80) cc_final: 0.7985 (ttp-170) REVERT: H 35 GLU cc_start: 0.7954 (tp30) cc_final: 0.6757 (mp0) outliers start: 22 outliers final: 10 residues processed: 156 average time/residue: 0.6210 time to fit residues: 104.5104 Evaluate side-chains 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 260 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 102 optimal weight: 0.2980 chunk 37 optimal weight: 0.0670 chunk 107 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN B 117 ASN G 155 ASN H 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.136116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.099458 restraints weight = 17934.102| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.95 r_work: 0.2878 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11176 Z= 0.117 Angle : 0.459 5.123 15378 Z= 0.263 Chirality : 0.041 0.144 1708 Planarity : 0.003 0.027 1676 Dihedral : 21.792 60.624 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.64 % Allowed : 17.08 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1130 helix: 1.74 (0.22), residues: 498 sheet: 0.01 (0.35), residues: 194 loop : -1.02 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 20 TYR 0.009 0.001 TYR B 83 PHE 0.006 0.001 PHE A 100 TRP 0.016 0.001 TRP B 131 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (11160) covalent geometry : angle 0.45946 / 0.26 (15374) hydrogen bonds : bond 0.03161 / 2.12 ( 576) hydrogen bonds : angle 4.28741 / 3.06 ( 1568) metal coordination : bond 0.00206 / 0.13 ( 16) metal coordination : angle 0.32579 / 0.25 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.379 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 20 ARG cc_start: 0.8815 (ttm-80) cc_final: 0.8030 (ttp-170) REVERT: B 35 GLU cc_start: 0.7921 (tp30) cc_final: 0.6771 (mp0) REVERT: G 20 ARG cc_start: 0.8816 (ttm-80) cc_final: 0.8031 (ttp-170) REVERT: H 35 GLU cc_start: 0.7924 (tp30) cc_final: 0.6761 (mp0) outliers start: 16 outliers final: 10 residues processed: 158 average time/residue: 0.6111 time to fit residues: 104.6576 Evaluate side-chains 154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 260 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 44 optimal weight: 0.0770 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 81 optimal weight: 0.0980 chunk 67 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 117 ASN H 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.137339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.103202 restraints weight = 11852.837| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.53 r_work: 0.2950 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11176 Z= 0.116 Angle : 0.469 6.028 15378 Z= 0.266 Chirality : 0.041 0.146 1708 Planarity : 0.003 0.028 1676 Dihedral : 21.756 60.424 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.84 % Allowed : 17.38 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.69 (0.25), residues: 1130 helix: 1.83 (0.22), residues: 500 sheet: 0.08 (0.35), residues: 194 loop : -0.98 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 199 TYR 0.010 0.001 TYR B 83 PHE 0.006 0.001 PHE B 26 TRP 0.016 0.001 TRP H 131 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (11160) covalent geometry : angle 0.46881 / 0.27 (15374) hydrogen bonds : bond 0.03138 / 2.11 ( 576) hydrogen bonds : angle 4.24388 / 3.03 ( 1568) metal coordination : bond 0.00239 / 0.12 ( 16) metal coordination : angle 0.47339 / 0.38 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.408 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 20 ARG cc_start: 0.8807 (ttm-80) cc_final: 0.8089 (ttp-170) REVERT: B 26 PHE cc_start: 0.8799 (m-10) cc_final: 0.8485 (m-10) REVERT: B 35 GLU cc_start: 0.7885 (tp30) cc_final: 0.6808 (mp0) REVERT: G 20 ARG cc_start: 0.8790 (ttm-80) cc_final: 0.8075 (ttp-170) REVERT: H 26 PHE cc_start: 0.8794 (m-10) cc_final: 0.8479 (m-10) REVERT: H 35 GLU cc_start: 0.7884 (tp30) cc_final: 0.6810 (mp0) outliers start: 18 outliers final: 12 residues processed: 160 average time/residue: 0.5516 time to fit residues: 95.3983 Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 117 ASN Chi-restraints excluded: chain I residue 260 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 148 GLN A 155 ASN B 117 ASN G 114 HIS G 148 GLN G 155 ASN H 117 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.097419 restraints weight = 17866.468| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.90 r_work: 0.2845 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11176 Z= 0.240 Angle : 0.532 7.670 15378 Z= 0.298 Chirality : 0.044 0.143 1708 Planarity : 0.003 0.029 1676 Dihedral : 21.927 61.033 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.64 % Allowed : 18.20 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.51 (0.24), residues: 1130 helix: 1.61 (0.22), residues: 500 sheet: -0.00 (0.35), residues: 194 loop : -0.99 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 20 TYR 0.012 0.002 TYR B 83 PHE 0.011 0.002 PHE A 185 TRP 0.018 0.002 TRP H 131 HIS 0.003 0.001 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (11160) covalent geometry : angle 0.53190 / 0.30 (15374) hydrogen bonds : bond 0.03713 / 2.46 ( 576) hydrogen bonds : angle 4.38413 / 3.11 ( 1568) metal coordination : bond 0.00719 / 0.45 ( 16) metal coordination : angle 1.08717 / 0.77 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.334 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 20 ARG cc_start: 0.8838 (ttm-80) cc_final: 0.7994 (ttp-170) REVERT: B 26 PHE cc_start: 0.8706 (m-10) cc_final: 0.8390 (m-10) REVERT: B 35 GLU cc_start: 0.7946 (tp30) cc_final: 0.6754 (mp0) REVERT: G 20 ARG cc_start: 0.8824 (ttm-80) cc_final: 0.7978 (ttp-170) REVERT: H 26 PHE cc_start: 0.8701 (m-10) cc_final: 0.8383 (m-10) REVERT: H 35 GLU cc_start: 0.7951 (tp30) cc_final: 0.6755 (mp0) outliers start: 16 outliers final: 8 residues processed: 152 average time/residue: 0.6176 time to fit residues: 101.1344 Evaluate side-chains 151 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 0.9990 chunk 84 optimal weight: 0.0270 chunk 57 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 14 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 94 optimal weight: 0.0070 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 148 GLN A 155 ASN B 117 ASN C 221 GLN G 114 HIS G 148 GLN G 155 ASN H 117 ASN I 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.102387 restraints weight = 11900.330| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.53 r_work: 0.2957 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11176 Z= 0.115 Angle : 0.494 8.287 15378 Z= 0.276 Chirality : 0.042 0.146 1708 Planarity : 0.003 0.028 1676 Dihedral : 21.894 60.737 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.23 % Allowed : 18.71 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.70 (0.25), residues: 1130 helix: 1.81 (0.22), residues: 500 sheet: 0.09 (0.35), residues: 194 loop : -0.95 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 262 TYR 0.010 0.001 TYR H 83 PHE 0.006 0.001 PHE A 100 TRP 0.016 0.001 TRP B 131 HIS 0.002 0.001 HIS G 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (11160) covalent geometry : angle 0.49417 / 0.28 (15374) hydrogen bonds : bond 0.03208 / 2.16 ( 576) hydrogen bonds : angle 4.28760 / 3.06 ( 1568) metal coordination : bond 0.00278 / 0.16 ( 16) metal coordination : angle 0.37570 / 0.31 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.296 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 20 ARG cc_start: 0.8800 (ttm-80) cc_final: 0.8075 (ttp-170) REVERT: B 26 PHE cc_start: 0.8774 (m-10) cc_final: 0.8477 (m-10) REVERT: B 35 GLU cc_start: 0.7858 (tp30) cc_final: 0.6803 (mp0) REVERT: C 262 ARG cc_start: 0.9008 (tpt90) cc_final: 0.8733 (tpt170) REVERT: G 20 ARG cc_start: 0.8790 (ttm-80) cc_final: 0.8067 (ttp-170) REVERT: H 26 PHE cc_start: 0.8776 (m-10) cc_final: 0.8479 (m-10) REVERT: H 35 GLU cc_start: 0.7859 (tp30) cc_final: 0.6809 (mp0) REVERT: I 262 ARG cc_start: 0.9008 (tpt90) cc_final: 0.8731 (tpt170) outliers start: 12 outliers final: 8 residues processed: 146 average time/residue: 0.5143 time to fit residues: 81.1400 Evaluate side-chains 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 117 ASN A 148 GLN A 155 ASN B 117 ASN C 221 GLN G 114 HIS G 117 ASN G 148 GLN G 155 ASN H 117 ASN I 221 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.135972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.101273 restraints weight = 13526.241| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.61 r_work: 0.2932 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11176 Z= 0.136 Angle : 0.485 8.218 15378 Z= 0.273 Chirality : 0.042 0.145 1708 Planarity : 0.003 0.029 1676 Dihedral : 21.831 60.985 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.23 % Allowed : 18.81 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.74 (0.25), residues: 1130 helix: 1.80 (0.22), residues: 500 sheet: 0.14 (0.35), residues: 194 loop : -0.88 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 262 TYR 0.010 0.001 TYR B 83 PHE 0.006 0.001 PHE G 185 TRP 0.020 0.001 TRP B 131 HIS 0.002 0.001 HIS A 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (11160) covalent geometry : angle 0.48518 / 0.27 (15374) hydrogen bonds : bond 0.03273 / 2.20 ( 576) hydrogen bonds : angle 4.27629 / 3.05 ( 1568) metal coordination : bond 0.00293 / 0.18 ( 16) metal coordination : angle 0.52621 / 0.43 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4121.18 seconds wall clock time: 70 minutes 55.18 seconds (4255.18 seconds total)