Starting phenix.real_space_refine on Fri Jul 3 00:09:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6puw_20483/07_2026/6puw_20483.cif Found real_map, /net/cci-nas-00/data/ceres_data/6puw_20483/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/6puw_20483/07_2026/6puw_20483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6puw_20483/07_2026/6puw_20483.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6puw_20483/07_2026/6puw_20483.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6puw_20483/07_2026/6puw_20483.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6puw_20483/07_2026/6puw_20483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6puw_20483/07_2026/6puw_20483.map" } 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-dev-6108/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: 2.41, per 1000 atoms: 0.22 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: 0.75 Conformation dependent library (CDL) restraints added in 279.5 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: 1.15 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: 2.17 Time building geometry restraints manager: 0.87 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=" CAW KLQ G 304 " pdb=" CAZ KLQ G 304 " ideal model delta sigma weight residual 1.366 1.542 -0.176 2.00e-02 2.50e+03 7.77e+01 ... (remaining 11155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 15138 2.38 - 4.76: 206 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: 0.01 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: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.980 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.590 ------------------------------------------------------------------------------- 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= 0.513 Angle : 0.707 13.487 15378 Z= 0.476 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 / 0.51 (11160) covalent geometry : angle 0.68985 / 0.47 (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 : 0.338 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: 0.5521 time to fit residues: 129.5509 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 : 0.277 ------------------------------------------------------------------------------- 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: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN C 221 GLN ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 HIS G 222 ASN I 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.132646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.097299 restraints weight = 14178.601| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.69 r_work: 0.2882 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 11176 Z= 0.264 Angle : 1.036 33.828 15378 Z= 0.550 Chirality : 0.056 0.459 1708 Planarity : 0.011 0.155 1676 Dihedral : 22.212 61.015 2150 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.81 % Favored : 95.93 % Rotamer: Outliers : 2.86 % Allowed : 11.35 % Favored : 85.79 % 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: -2.30 (0.22), residues: 1130 helix: -0.97 (0.21), residues: 496 sheet: -1.22 (0.32), residues: 192 loop : -2.18 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.002 ARG I 269 TYR 0.110 0.006 TYR H 99 PHE 0.085 0.005 PHE G 26 TRP 0.107 0.008 TRP G 61 HIS 0.037 0.004 HIS G 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.26 (11160) covalent geometry : angle 1.03614 / 0.55 (15374) hydrogen bonds : bond 0.05513 / 3.59 ( 576) hydrogen bonds : angle 5.71088 / 4.04 ( 1568) metal coordination : bond 0.03262 / 2.32 ( 16) metal coordination : angle 1.96326 / 1.72 ( 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 191 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.294 Fit side-chains 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: 0.8809 (ttm-80) cc_final: 0.7906 (ttp-170) REVERT: A 27 ASN cc_start: 0.8581 (p0) cc_final: 0.8289 (m110) REVERT: B 35 GLU cc_start: 0.8054 (tp30) cc_final: 0.6938 (mp0) REVERT: B 251 ILE cc_start: 0.8934 (mm) cc_final: 0.8475 (pp) REVERT: G 20 ARG cc_start: 0.8803 (ttm-80) cc_final: 0.8123 (ttp-170) REVERT: G 27 ASN cc_start: 0.8580 (p0) cc_final: 0.8307 (m110) REVERT: H 251 ILE cc_start: 0.8912 (mm) cc_final: 0.8441 (pp) REVERT: I 236 LYS cc_start: 0.8575 (mmtp) cc_final: 0.8367 (mmtp) outliers start: 28 outliers final: 5 residues processed: 179 average time/residue: 0.4752 time to fit residues: 91.7789 Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 154 MET Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain I residue 260 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 51 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 102 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 GLN C 221 GLN G 168 GLN H 221 GLN I 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.097181 restraints weight = 18109.027| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.95 r_work: 0.2858 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 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 = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1317 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= 0.138 Angle : 0.514 5.487 15378 Z= 0.293 Chirality : 0.043 0.151 1708 Planarity : 0.003 0.033 1676 Dihedral : 22.001 60.226 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.45 % Allowed : 12.99 % Favored : 84.56 % 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: -0.96 (0.23), residues: 1130 helix: 0.43 (0.22), residues: 498 sheet: -0.72 (0.33), residues: 194 loop : -1.81 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 20 TYR 0.012 0.001 TYR J 227 PHE 0.028 0.001 PHE G 121 TRP 0.019 0.001 TRP H 19 HIS 0.009 0.001 HIS G 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (11160) covalent geometry : angle 0.51382 / 0.29 (15374) hydrogen bonds : bond 0.03723 / 2.49 ( 576) hydrogen bonds : angle 4.81383 / 3.41 ( 1568) metal coordination : bond 0.00823 / 0.57 ( 16) metal coordination : angle 1.22222 / 1.10 ( 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 190 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.266 Fit side-chains 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: 0.8826 (ttm-80) cc_final: 0.7932 (ttp-170) REVERT: A 27 ASN cc_start: 0.8673 (p0) cc_final: 0.8465 (p0) REVERT: A 95 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: A 136 LYS cc_start: 0.8608 (tttm) cc_final: 0.8372 (tptp) REVERT: B 35 GLU cc_start: 0.8079 (tp30) cc_final: 0.6955 (mp0) REVERT: B 251 ILE cc_start: 0.8889 (mm) cc_final: 0.8623 (pp) REVERT: B 258 LYS cc_start: 0.8029 (ttmm) cc_final: 0.7643 (ttmm) REVERT: G 20 ARG cc_start: 0.8788 (ttm-80) cc_final: 0.8070 (ttp-170) REVERT: G 27 ASN cc_start: 0.8693 (p0) cc_final: 0.8489 (p0) REVERT: G 136 LYS cc_start: 0.8622 (tttm) cc_final: 0.8382 (tptp) REVERT: H 35 GLU cc_start: 0.8056 (tp30) cc_final: 0.6957 (mp0) REVERT: H 251 ILE cc_start: 0.8862 (mm) cc_final: 0.8602 (pp) REVERT: H 258 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7586 (ttmm) outliers start: 24 outliers final: 7 residues processed: 177 average time/residue: 0.4657 time to fit residues: 89.2304 Evaluate side-chains 164 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 A residue 260 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 0.0670 overall best weight: 1.4124 ------------------------------------------------------------------------------- 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 A 155 ASN B 117 ASN C 221 GLN G 114 HIS G 148 GLN G 155 ASN H 117 ASN H 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.130077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.094136 restraints weight = 15968.116| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.80 r_work: 0.2832 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11176 Z= 0.196 Angle : 0.520 6.082 15378 Z= 0.293 Chirality : 0.044 0.152 1708 Planarity : 0.003 0.038 1676 Dihedral : 22.038 60.722 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.86 % Allowed : 12.78 % Favored : 84.36 % 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: -0.44 (0.24), residues: 1130 helix: 0.90 (0.22), residues: 498 sheet: -0.53 (0.33), residues: 194 loop : -1.54 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 199 TYR 0.011 0.001 TYR B 83 PHE 0.014 0.002 PHE H 26 TRP 0.012 0.001 TRP H 19 HIS 0.007 0.001 HIS G 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (11160) covalent geometry : angle 0.51937 / 0.29 (15374) hydrogen bonds : bond 0.03847 / 2.54 ( 576) hydrogen bonds : angle 4.66405 / 3.31 ( 1568) metal coordination : bond 0.00957 / 0.62 ( 16) metal coordination : angle 1.47568 / 1.17 ( 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 194 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.337 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: 0.8832 (ttm-80) cc_final: 0.7932 (ttp-170) REVERT: A 27 ASN cc_start: 0.8672 (p0) cc_final: 0.8471 (p0) REVERT: A 136 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8362 (tptp) REVERT: B 35 GLU cc_start: 0.8055 (tp30) cc_final: 0.6906 (mp0) REVERT: B 154 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7495 (mmt) REVERT: B 258 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7723 (mtmt) REVERT: G 20 ARG cc_start: 0.8791 (ttm-80) cc_final: 0.7938 (ttp-170) REVERT: H 35 GLU cc_start: 0.8038 (tp30) cc_final: 0.6942 (mp0) REVERT: H 258 LYS cc_start: 0.8025 (ttmm) cc_final: 0.7708 (mtmt) outliers start: 28 outliers final: 12 residues processed: 175 average time/residue: 0.5047 time to fit residues: 95.2073 Evaluate side-chains 174 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 260 VAL 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 B residue 154 MET Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 150 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN C 221 GLN G 155 ASN I 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.096133 restraints weight = 17969.210| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.92 r_work: 0.2838 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11176 Z= 0.167 Angle : 0.500 5.159 15378 Z= 0.284 Chirality : 0.043 0.146 1708 Planarity : 0.003 0.039 1676 Dihedral : 22.019 60.696 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.94 % Allowed : 14.52 % Favored : 83.54 % 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: -0.12 (0.24), residues: 1130 helix: 1.19 (0.22), residues: 498 sheet: -0.43 (0.34), residues: 194 loop : -1.38 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 199 TYR 0.010 0.001 TYR A 194 PHE 0.011 0.001 PHE H 26 TRP 0.009 0.001 TRP H 19 HIS 0.005 0.001 HIS G 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (11160) covalent geometry : angle 0.49963 / 0.28 (15374) hydrogen bonds : bond 0.03616 / 2.39 ( 576) hydrogen bonds : angle 4.57350 / 3.25 ( 1568) metal coordination : bond 0.00715 / 0.46 ( 16) metal coordination : angle 1.20728 / 1.00 ( 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 180 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.358 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: 0.7955 (ttp-170) REVERT: A 95 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8526 (tt0) REVERT: A 136 LYS cc_start: 0.8644 (tttm) cc_final: 0.8397 (tptp) REVERT: B 35 GLU cc_start: 0.8039 (tp30) cc_final: 0.6897 (mp0) REVERT: G 20 ARG cc_start: 0.8806 (ttm-80) cc_final: 0.7981 (ttp-170) REVERT: H 35 GLU cc_start: 0.8061 (tp30) cc_final: 0.6955 (mp0) REVERT: H 244 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8103 (ttpt) outliers start: 19 outliers final: 10 residues processed: 168 average time/residue: 0.5327 time to fit residues: 96.1272 Evaluate side-chains 171 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 A residue 260 VAL 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 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 244 LYS 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: 0.9980 chunk 24 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN B 117 ASN C 221 GLN G 155 ASN I 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.095085 restraints weight = 19127.893| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.01 r_work: 0.2832 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11176 Z= 0.145 Angle : 0.485 5.251 15378 Z= 0.276 Chirality : 0.042 0.146 1708 Planarity : 0.003 0.038 1676 Dihedral : 21.968 60.906 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.15 % Allowed : 15.34 % Favored : 82.52 % 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: 0.17 (0.24), residues: 1130 helix: 1.44 (0.22), residues: 498 sheet: -0.27 (0.34), residues: 194 loop : -1.25 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 199 TYR 0.011 0.001 TYR B 83 PHE 0.008 0.001 PHE B 26 TRP 0.009 0.001 TRP H 131 HIS 0.004 0.001 HIS H 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (11160) covalent geometry : angle 0.48521 / 0.28 (15374) hydrogen bonds : bond 0.03422 / 2.27 ( 576) hydrogen bonds : angle 4.46867 / 3.18 ( 1568) metal coordination : bond 0.00584 / 0.39 ( 16) metal coordination : angle 0.83352 / 0.69 ( 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 178 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.385 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: 0.8825 (ttm-80) cc_final: 0.7943 (ttp-170) REVERT: A 136 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8396 (tptp) REVERT: B 35 GLU cc_start: 0.7997 (tp30) cc_final: 0.6787 (mp0) REVERT: G 20 ARG cc_start: 0.8799 (ttm-80) cc_final: 0.7954 (ttp-170) REVERT: G 154 MET cc_start: 0.9325 (mmt) cc_final: 0.9107 (mmt) REVERT: H 35 GLU cc_start: 0.8043 (tp30) cc_final: 0.6883 (mp0) outliers start: 21 outliers final: 10 residues processed: 167 average time/residue: 0.5097 time to fit residues: 91.8487 Evaluate side-chains 162 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 150 VAL 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: 0.8980 chunk 37 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN B 117 ASN C 221 GLN G 155 ASN I 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.097756 restraints weight = 17906.289| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.92 r_work: 0.2850 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1701 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= 0.147 Angle : 0.484 5.138 15378 Z= 0.276 Chirality : 0.042 0.143 1708 Planarity : 0.003 0.037 1676 Dihedral : 21.938 60.920 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 : 1.94 % Allowed : 16.46 % Favored : 81.60 % 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: 0.30 (0.24), residues: 1130 helix: 1.52 (0.22), residues: 498 sheet: -0.19 (0.35), residues: 194 loop : -1.15 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 199 TYR 0.010 0.001 TYR B 83 PHE 0.007 0.001 PHE A 185 TRP 0.012 0.001 TRP B 131 HIS 0.002 0.001 HIS A 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (11160) covalent geometry : angle 0.48346 / 0.28 (15374) hydrogen bonds : bond 0.03424 / 2.26 ( 576) hydrogen bonds : angle 4.41908 / 3.15 ( 1568) metal coordination : bond 0.00590 / 0.36 ( 16) metal coordination : angle 1.00882 / 0.78 ( 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 165 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.278 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: 0.8827 (ttm-80) cc_final: 0.8049 (ttp-170) REVERT: A 136 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8406 (tptp) REVERT: B 35 GLU cc_start: 0.8019 (tp30) cc_final: 0.6829 (mp0) REVERT: G 20 ARG cc_start: 0.8816 (ttm-80) cc_final: 0.7974 (ttp-170) REVERT: H 35 GLU cc_start: 0.7993 (tp30) cc_final: 0.6801 (mp0) REVERT: H 244 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7950 (ttpt) outliers start: 19 outliers final: 9 residues processed: 155 average time/residue: 0.5230 time to fit residues: 87.3414 Evaluate side-chains 155 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 136 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 H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 244 LYS 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: 0.0970 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 0.0040 chunk 36 optimal weight: 0.9980 chunk 81 optimal weight: 0.0980 chunk 67 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN B 117 ASN C 221 GLN G 155 ASN H 117 ASN H 221 GLN I 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.137438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.103446 restraints weight = 11844.741| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.53 r_work: 0.2972 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1916 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= 0.102 Angle : 0.455 5.566 15378 Z= 0.261 Chirality : 0.041 0.144 1708 Planarity : 0.003 0.034 1676 Dihedral : 21.764 60.343 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.64 % Allowed : 16.87 % Favored : 81.49 % 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: 0.62 (0.25), residues: 1130 helix: 1.80 (0.23), residues: 498 sheet: 0.06 (0.35), residues: 194 loop : -1.07 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 20 TYR 0.009 0.001 TYR G 83 PHE 0.013 0.001 PHE H 26 TRP 0.019 0.001 TRP H 131 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.10 (11160) covalent geometry : angle 0.45516 / 0.26 (15374) hydrogen bonds : bond 0.03077 / 2.07 ( 576) hydrogen bonds : angle 4.26501 / 3.05 ( 1568) metal coordination : bond 0.00184 / 0.09 ( 16) metal coordination : angle 0.96918 / 0.58 ( 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 175 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.418 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: 0.8788 (ttm-80) cc_final: 0.8043 (ttp-170) REVERT: B 26 PHE cc_start: 0.8759 (m-10) cc_final: 0.8430 (m-10) REVERT: B 35 GLU cc_start: 0.7893 (tp30) cc_final: 0.6809 (mp0) REVERT: G 20 ARG cc_start: 0.8759 (ttm-80) cc_final: 0.8013 (ttp-170) REVERT: H 16 HIS cc_start: 0.7491 (m-70) cc_final: 0.7092 (m90) REVERT: H 35 GLU cc_start: 0.7833 (tp30) cc_final: 0.6754 (mp0) outliers start: 16 outliers final: 9 residues processed: 166 average time/residue: 0.4775 time to fit residues: 85.7265 Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 24 optimal weight: 0.0060 chunk 50 optimal weight: 0.9980 chunk 94 optimal weight: 0.0870 chunk 6 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 148 GLN A 155 ASN B 117 ASN B 168 GLN G 114 HIS G 148 GLN G 155 ASN H 117 ASN H 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.101571 restraints weight = 17850.031| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.93 r_work: 0.2887 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11176 Z= 0.113 Angle : 0.465 7.278 15378 Z= 0.266 Chirality : 0.041 0.144 1708 Planarity : 0.003 0.034 1676 Dihedral : 21.690 60.188 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.33 % Allowed : 17.69 % Favored : 80.98 % 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: 0.71 (0.25), residues: 1130 helix: 1.84 (0.23), residues: 500 sheet: 0.19 (0.35), residues: 194 loop : -1.01 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 187 TYR 0.009 0.001 TYR B 83 PHE 0.006 0.001 PHE H 100 TRP 0.017 0.001 TRP B 131 HIS 0.002 0.001 HIS G 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (11160) covalent geometry : angle 0.46482 / 0.27 (15374) hydrogen bonds : bond 0.03113 / 2.08 ( 576) hydrogen bonds : angle 4.22395 / 3.01 ( 1568) metal coordination : bond 0.00235 / 0.13 ( 16) metal coordination : angle 0.47446 / 0.39 ( 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: 13 poor density : 147 time to evaluate : 0.294 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: 0.8819 (ttm-80) cc_final: 0.8058 (ttp-170) REVERT: B 26 PHE cc_start: 0.8708 (m-10) cc_final: 0.8423 (m-10) REVERT: B 35 GLU cc_start: 0.7925 (tp30) cc_final: 0.6750 (mp0) REVERT: G 20 ARG cc_start: 0.8782 (ttm-80) cc_final: 0.8062 (ttp-170) REVERT: G 154 MET cc_start: 0.9300 (mmt) cc_final: 0.9044 (mmt) REVERT: H 16 HIS cc_start: 0.7482 (m-70) cc_final: 0.7086 (m90) REVERT: H 35 GLU cc_start: 0.7866 (tp30) cc_final: 0.6690 (mp0) outliers start: 13 outliers final: 11 residues processed: 152 average time/residue: 0.4870 time to fit residues: 80.0324 Evaluate side-chains 154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 0.7980 chunk 84 optimal weight: 0.4980 chunk 57 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 94 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 148 GLN B 168 GLN G 114 HIS G 148 GLN G 155 ASN H 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.136696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.102655 restraints weight = 11955.229| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.53 r_work: 0.2946 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 11176 Z= 0.190 Angle : 0.996 59.200 15378 Z= 0.621 Chirality : 0.042 0.207 1708 Planarity : 0.003 0.043 1676 Dihedral : 21.691 60.181 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.33 % Allowed : 17.69 % Favored : 80.98 % Cbeta Deviations : 0.19 % 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: 1.86 (0.23), residues: 498 sheet: 0.20 (0.35), residues: 194 loop : -1.07 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 187 TYR 0.009 0.001 TYR B 83 PHE 0.006 0.001 PHE B 26 TRP 0.015 0.001 TRP B 131 HIS 0.002 0.001 HIS G 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.19 (11160) covalent geometry : angle 0.99654 / 0.62 (15374) hydrogen bonds : bond 0.03116 / 2.09 ( 576) hydrogen bonds : angle 4.22304 / 3.01 ( 1568) metal coordination : bond 0.00205 / 0.12 ( 16) metal coordination : angle 0.47133 / 0.38 ( 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 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.290 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: 0.8811 (ttm-80) cc_final: 0.8121 (ttp-170) REVERT: B 35 GLU cc_start: 0.7873 (tp30) cc_final: 0.6805 (mp0) REVERT: G 20 ARG cc_start: 0.8774 (ttm-80) cc_final: 0.8114 (ttp-170) REVERT: H 16 HIS cc_start: 0.7515 (m-70) cc_final: 0.7132 (m90) REVERT: H 35 GLU cc_start: 0.7817 (tp30) cc_final: 0.6747 (mp0) outliers start: 13 outliers final: 10 residues processed: 149 average time/residue: 0.5030 time to fit residues: 80.7848 Evaluate side-chains 153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 260 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 148 GLN B 117 ASN B 168 GLN C 221 GLN G 114 HIS G 148 GLN G 155 ASN H 221 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.101253 restraints weight = 13597.416| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.64 r_work: 0.2935 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- 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 = 0.49 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 = 0.49 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: 0.8983 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 11176 Z= 0.190 Angle : 0.996 59.200 15378 Z= 0.621 Chirality : 0.042 0.207 1708 Planarity : 0.003 0.043 1676 Dihedral : 21.691 60.181 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.12 % Allowed : 17.89 % Favored : 80.98 % Cbeta Deviations : 0.19 % 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: 1.86 (0.23), residues: 498 sheet: 0.20 (0.35), residues: 194 loop : -1.07 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 187 TYR 0.009 0.001 TYR B 83 PHE 0.006 0.001 PHE B 26 TRP 0.015 0.001 TRP B 131 HIS 0.002 0.001 HIS G 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.19 (11160) covalent geometry : angle 0.99654 / 0.62 (15374) hydrogen bonds : bond 0.03116 / 2.09 ( 576) hydrogen bonds : angle 4.22304 / 3.01 ( 1568) metal coordination : bond 0.00205 / 0.12 ( 16) metal coordination : angle 0.47133 / 0.38 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3449.32 seconds wall clock time: 59 minutes 27.26 seconds (3567.26 seconds total)