Starting phenix.real_space_refine on Sat Aug 23 09:05:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6puw_20483/08_2025/6puw_20483.cif Found real_map, /net/cci-nas-00/data/ceres_data/6puw_20483/08_2025/6puw_20483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6puw_20483/08_2025/6puw_20483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6puw_20483/08_2025/6puw_20483.map" model { file = "/net/cci-nas-00/data/ceres_data/6puw_20483/08_2025/6puw_20483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6puw_20483/08_2025/6puw_20483.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.024 sd= 0.693 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 72 5.49 5 Mg 4 5.21 5 S 34 5.16 5 C 6662 2.51 5 N 1914 2.21 5 O 2420 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.26, per 1000 atoms: 0.29 Number of scatterers: 11116 At special positions: 0 Unit cell: (92.43, 133.51, 83.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 34 16.00 P 72 15.00 Mg 4 11.99 F 6 9.00 O 2420 8.00 N 1914 7.00 C 6662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 370.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.49 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: 2.21 Time building geometry restraints manager: 1.34 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: 15184 2.38 - 4.76: 160 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=" C LYS A 127 " pdb=" N ALA A 128 " pdb=" CA ALA A 128 " ideal model delta sigma weight residual 120.29 126.31 -6.02 1.42e+00 4.96e-01 1.80e+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: 1510 0.067 - 0.134: 182 0.134 - 0.201: 10 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: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.620 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 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= 0.443 Angle : 0.663 13.487 15378 Z= 0.377 Chirality : 0.046 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 aren 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 covalent geometry : bond 0.00863 (11160) covalent geometry : angle 0.64469 (15374) hydrogen bonds : bond 0.14024 ( 576) hydrogen bonds : angle 6.65583 ( 1568) metal coordination : bond 0.08287 ( 16) metal coordination : angle 9.59377 ( 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 : 0.410 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: 0.6967 time to fit residues: 163.0745 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 : 0.366 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 214 GLN G 222 ASN H 164 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 = 0.3495 r_free = 0.3495 target = 0.135104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.099716 restraints weight = 14303.084| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.72 r_work: 0.2954 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 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 = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11176 Z= 0.206 Angle : 0.844 13.297 15378 Z= 0.462 Chirality : 0.054 0.407 1708 Planarity : 0.010 0.158 1676 Dihedral : 22.173 61.938 2150 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.34 % Favored : 95.31 % Rotamer: Outliers : 3.07 % Allowed : 10.53 % Favored : 86.40 % 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 aren not related in a simple way. whole: -2.28 (0.22), residues: 1130 helix: -0.97 (0.21), residues: 498 sheet: -1.25 (0.32), residues: 194 loop : -2.13 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG I 269 TYR 0.112 0.006 TYR H 99 PHE 0.084 0.005 PHE G 26 TRP 0.106 0.008 TRP G 61 HIS 0.037 0.004 HIS H 12 Details of bonding type rmsd covalent geometry : bond 0.00460 (11160) covalent geometry : angle 0.84245 (15374) hydrogen bonds : bond 0.04684 ( 576) hydrogen bonds : angle 5.59669 ( 1568) metal coordination : bond 0.01348 ( 16) metal coordination : angle 3.32353 ( 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 203 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.342 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: 0.8828 (ttm-80) cc_final: 0.8084 (ttp-170) REVERT: A 27 ASN cc_start: 0.8639 (p0) cc_final: 0.8372 (m110) REVERT: B 35 GLU cc_start: 0.8102 (tp30) cc_final: 0.7090 (mp0) REVERT: B 251 ILE cc_start: 0.8975 (mm) cc_final: 0.8665 (pp) REVERT: G 10 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7843 (tm-30) REVERT: G 136 LYS cc_start: 0.8597 (tttm) cc_final: 0.8395 (tptp) REVERT: H 26 PHE cc_start: 0.8781 (m-80) cc_final: 0.8580 (m-10) REVERT: H 251 ILE cc_start: 0.8948 (mm) cc_final: 0.8633 (pp) REVERT: H 258 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7708 (ttmm) REVERT: I 236 LYS cc_start: 0.8602 (mmtp) cc_final: 0.8388 (mmtp) REVERT: I 262 ARG cc_start: 0.9088 (tpt90) cc_final: 0.8844 (tpt170) REVERT: J 236 LYS cc_start: 0.9018 (mptt) cc_final: 0.8803 (pttt) outliers start: 30 outliers final: 6 residues processed: 185 average time/residue: 0.5963 time to fit residues: 118.7967 Evaluate side-chains 159 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 28 LEU 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: 0.5980 chunk 114 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN A 168 GLN B 117 ASN C 221 GLN ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 GLN H 221 GLN I 221 GLN J 222 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.097218 restraints weight = 18231.962| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.96 r_work: 0.2916 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11176 Z= 0.140 Angle : 0.494 8.793 15378 Z= 0.279 Chirality : 0.041 0.149 1708 Planarity : 0.004 0.053 1676 Dihedral : 21.808 60.851 2148 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.97 % Allowed : 12.37 % Favored : 84.66 % 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 aren not related in a simple way. whole: -0.97 (0.23), residues: 1130 helix: 0.43 (0.22), residues: 500 sheet: -0.73 (0.33), residues: 194 loop : -1.84 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 199 TYR 0.010 0.001 TYR B 83 PHE 0.018 0.001 PHE H 26 TRP 0.016 0.001 TRP H 19 HIS 0.007 0.001 HIS G 171 Details of bonding type rmsd covalent geometry : bond 0.00315 (11160) covalent geometry : angle 0.49388 (15374) hydrogen bonds : bond 0.03440 ( 576) hydrogen bonds : angle 4.71265 ( 1568) metal coordination : bond 0.00566 ( 16) metal coordination : angle 1.27008 ( 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 196 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.267 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: 0.8838 (ttm-80) cc_final: 0.8068 (ttp-170) REVERT: A 136 LYS cc_start: 0.8662 (tttm) cc_final: 0.8446 (tptp) REVERT: B 35 GLU cc_start: 0.8029 (tp30) cc_final: 0.6946 (mp0) REVERT: B 258 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7830 (mtpt) REVERT: G 20 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8214 (ttm110) REVERT: G 136 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8404 (tptp) REVERT: H 35 GLU cc_start: 0.8020 (tp30) cc_final: 0.7727 (tp30) REVERT: H 252 GLN cc_start: 0.8354 (tt0) cc_final: 0.8061 (tt0) REVERT: H 258 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7781 (mtmt) REVERT: I 231 ARG cc_start: 0.8073 (tpt-90) cc_final: 0.7841 (ttt90) outliers start: 29 outliers final: 8 residues processed: 182 average time/residue: 0.6051 time to fit residues: 117.9428 Evaluate side-chains 165 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 20 ARG Chi-restraints excluded: chain G residue 136 LYS Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 213 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 117 ASN G 155 ASN G 214 GLN H 117 ASN H 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.131471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.095168 restraints weight = 16068.859| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.84 r_work: 0.2834 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- 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 = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11176 Z= 0.204 Angle : 0.503 6.121 15378 Z= 0.286 Chirality : 0.043 0.148 1708 Planarity : 0.004 0.038 1676 Dihedral : 21.838 61.725 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.56 % Allowed : 13.91 % 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 aren not related in a simple way. whole: -0.30 (0.24), residues: 1130 helix: 0.98 (0.22), residues: 498 sheet: -0.47 (0.33), residues: 194 loop : -1.41 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 199 TYR 0.012 0.001 TYR A 194 PHE 0.016 0.001 PHE G 121 TRP 0.011 0.001 TRP H 19 HIS 0.005 0.001 HIS G 171 Details of bonding type rmsd covalent geometry : bond 0.00473 (11160) covalent geometry : angle 0.50253 (15374) hydrogen bonds : bond 0.03600 ( 576) hydrogen bonds : angle 4.56856 ( 1568) metal coordination : bond 0.00873 ( 16) metal coordination : angle 1.60726 ( 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 179 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.301 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: 0.8837 (ttm-80) cc_final: 0.7976 (ttp-170) REVERT: A 95 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: B 35 GLU cc_start: 0.7994 (tp30) cc_final: 0.6809 (mp0) REVERT: G 10 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7906 (tm-30) REVERT: G 20 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8189 (ttm110) REVERT: G 136 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8379 (tptp) REVERT: H 35 GLU cc_start: 0.8031 (tp30) cc_final: 0.7704 (tp30) REVERT: H 252 GLN cc_start: 0.8363 (tt0) cc_final: 0.7974 (tt0) REVERT: I 231 ARG cc_start: 0.8175 (tpt-90) cc_final: 0.7959 (ttt90) outliers start: 25 outliers final: 10 residues processed: 165 average time/residue: 0.5666 time to fit residues: 100.5257 Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 153 SER Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 136 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 117 ASN Chi-restraints excluded: chain I residue 213 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 17 optimal weight: 0.0470 chunk 46 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 111 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS A 148 GLN A 155 ASN B 117 ASN C 221 GLN 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 = 0.3497 r_free = 0.3497 target = 0.135442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.099266 restraints weight = 18048.728| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.95 r_work: 0.2910 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11176 Z= 0.118 Angle : 0.456 5.976 15378 Z= 0.263 Chirality : 0.040 0.146 1708 Planarity : 0.003 0.039 1676 Dihedral : 21.628 61.922 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.35 % Allowed : 15.03 % Favored : 82.62 % 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 aren not related in a simple way. whole: 0.19 (0.24), residues: 1130 helix: 1.45 (0.23), residues: 498 sheet: -0.22 (0.34), residues: 194 loop : -1.25 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 262 TYR 0.009 0.001 TYR B 83 PHE 0.009 0.001 PHE B 26 TRP 0.009 0.001 TRP B 131 HIS 0.003 0.001 HIS G 171 Details of bonding type rmsd covalent geometry : bond 0.00254 (11160) covalent geometry : angle 0.45631 (15374) hydrogen bonds : bond 0.03052 ( 576) hydrogen bonds : angle 4.35522 ( 1568) metal coordination : bond 0.00263 ( 16) metal coordination : angle 0.73312 ( 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 173 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.412 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: 0.8798 (ttm-80) cc_final: 0.8049 (ttp-170) REVERT: A 136 LYS cc_start: 0.8644 (tttm) cc_final: 0.8403 (tptp) REVERT: B 35 GLU cc_start: 0.7917 (tp30) cc_final: 0.6747 (mp0) REVERT: G 10 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7892 (tm-30) REVERT: G 20 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8163 (ttm110) REVERT: G 136 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8380 (tptp) REVERT: H 35 GLU cc_start: 0.8003 (tp30) cc_final: 0.7648 (tp30) REVERT: H 252 GLN cc_start: 0.8256 (tt0) cc_final: 0.7864 (tt0) REVERT: I 231 ARG cc_start: 0.8185 (tpt-90) cc_final: 0.7949 (ttt90) outliers start: 23 outliers final: 11 residues processed: 163 average time/residue: 0.6055 time to fit residues: 106.3340 Evaluate side-chains 155 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 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 20 ARG Chi-restraints excluded: chain G residue 136 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 213 LEU 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: 0.9990 chunk 24 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN B 117 ASN G 155 ASN H 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.096928 restraints weight = 19182.436| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.02 r_work: 0.2864 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1820 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= 0.153 Angle : 0.465 6.060 15378 Z= 0.267 Chirality : 0.041 0.144 1708 Planarity : 0.003 0.040 1676 Dihedral : 21.645 62.204 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.25 % Allowed : 15.54 % Favored : 82.21 % 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 aren not related in a simple way. whole: 0.36 (0.24), residues: 1130 helix: 1.58 (0.22), residues: 498 sheet: -0.12 (0.34), 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 0.011 0.001 TYR B 83 PHE 0.008 0.001 PHE G 121 TRP 0.011 0.001 TRP B 131 HIS 0.003 0.001 HIS G 171 Details of bonding type rmsd covalent geometry : bond 0.00349 (11160) covalent geometry : angle 0.46518 (15374) hydrogen bonds : bond 0.03192 ( 576) hydrogen bonds : angle 4.33633 ( 1568) metal coordination : bond 0.00542 ( 16) metal coordination : angle 1.05565 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.428 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: 0.8857 (ttm-80) cc_final: 0.8086 (ttp-170) REVERT: A 154 MET cc_start: 0.9430 (mmt) cc_final: 0.9171 (mmt) REVERT: B 35 GLU cc_start: 0.7954 (tp30) cc_final: 0.6852 (mp0) REVERT: G 20 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8262 (ttm110) REVERT: G 136 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8406 (tptp) REVERT: H 35 GLU cc_start: 0.8020 (tp30) cc_final: 0.7018 (mp0) REVERT: I 231 ARG cc_start: 0.8238 (tpt-90) cc_final: 0.7982 (ttt90) outliers start: 22 outliers final: 11 residues processed: 158 average time/residue: 0.6073 time to fit residues: 103.3808 Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 136 LYS Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 213 LEU 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: 0.0020 chunk 37 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 117 ASN G 155 ASN H 117 ASN H 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.099580 restraints weight = 18008.181| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.93 r_work: 0.2887 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11176 Z= 0.132 Angle : 0.457 5.969 15378 Z= 0.262 Chirality : 0.041 0.145 1708 Planarity : 0.003 0.039 1676 Dihedral : 21.578 62.177 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.45 % Allowed : 16.16 % Favored : 81.39 % 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 aren not related in a simple way. whole: 0.52 (0.25), residues: 1130 helix: 1.71 (0.23), residues: 498 sheet: -0.00 (0.34), residues: 194 loop : -1.10 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 262 TYR 0.010 0.001 TYR B 83 PHE 0.007 0.001 PHE G 100 TRP 0.011 0.001 TRP B 131 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00296 (11160) covalent geometry : angle 0.45659 (15374) hydrogen bonds : bond 0.03039 ( 576) hydrogen bonds : angle 4.27736 ( 1568) metal coordination : bond 0.00294 ( 16) metal coordination : angle 0.54854 ( 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 172 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.446 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: 0.8821 (ttm-80) cc_final: 0.7989 (ttp-170) REVERT: A 136 LYS cc_start: 0.8648 (tttm) cc_final: 0.8402 (tptp) REVERT: B 35 GLU cc_start: 0.7895 (tp30) cc_final: 0.6744 (mp0) REVERT: G 20 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8137 (ttm110) REVERT: G 136 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8349 (tptp) REVERT: H 16 HIS cc_start: 0.7544 (m-70) cc_final: 0.7182 (m90) REVERT: H 35 GLU cc_start: 0.7981 (tp30) cc_final: 0.6783 (mp0) outliers start: 24 outliers final: 14 residues processed: 158 average time/residue: 0.6629 time to fit residues: 112.6806 Evaluate side-chains 160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 136 LYS Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 230 SER 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: 0.0070 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 117 ASN G 155 ASN H 117 ASN H 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.102662 restraints weight = 11892.755| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.52 r_work: 0.2974 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1947 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= 0.135 Angle : 0.459 8.080 15378 Z= 0.262 Chirality : 0.041 0.144 1708 Planarity : 0.003 0.038 1676 Dihedral : 21.559 62.269 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.25 % Allowed : 16.46 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.25), residues: 1130 helix: 1.74 (0.22), residues: 500 sheet: 0.09 (0.35), residues: 194 loop : -1.02 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 262 TYR 0.011 0.001 TYR B 83 PHE 0.006 0.001 PHE G 100 TRP 0.017 0.001 TRP H 131 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00305 (11160) covalent geometry : angle 0.45927 (15374) hydrogen bonds : bond 0.03029 ( 576) hydrogen bonds : angle 4.25869 ( 1568) metal coordination : bond 0.00359 ( 16) metal coordination : angle 0.52309 ( 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 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.519 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: 0.8804 (ttm-80) cc_final: 0.8044 (ttp-170) REVERT: A 136 LYS cc_start: 0.8654 (tttm) cc_final: 0.8427 (tptp) REVERT: B 26 PHE cc_start: 0.8772 (m-10) cc_final: 0.8482 (m-10) REVERT: B 35 GLU cc_start: 0.7836 (tp30) cc_final: 0.6774 (mp0) REVERT: G 20 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8268 (ttp-170) REVERT: G 136 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8369 (tptp) REVERT: H 16 HIS cc_start: 0.7544 (m-70) cc_final: 0.7193 (m90) REVERT: H 35 GLU cc_start: 0.7882 (tp30) cc_final: 0.6863 (mp0) outliers start: 22 outliers final: 13 residues processed: 155 average time/residue: 0.6789 time to fit residues: 113.0191 Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 136 LYS Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 230 SER 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: 1.9990 chunk 58 optimal weight: 10.0000 chunk 24 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 94 optimal weight: 0.0570 chunk 6 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS A 148 GLN A 155 ASN B 117 ASN H 117 ASN H 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.101687 restraints weight = 17766.033| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.93 r_work: 0.2951 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11176 Z= 0.122 Angle : 0.457 7.178 15378 Z= 0.261 Chirality : 0.040 0.146 1708 Planarity : 0.003 0.037 1676 Dihedral : 21.457 62.204 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.74 % Allowed : 17.08 % Favored : 81.19 % 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 aren not related in a simple way. whole: 0.71 (0.25), residues: 1130 helix: 1.81 (0.23), residues: 502 sheet: 0.20 (0.35), residues: 194 loop : -1.00 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 262 TYR 0.009 0.001 TYR B 83 PHE 0.006 0.001 PHE H 26 TRP 0.020 0.001 TRP B 131 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00272 (11160) covalent geometry : angle 0.45705 (15374) hydrogen bonds : bond 0.02913 ( 576) hydrogen bonds : angle 4.19588 ( 1568) metal coordination : bond 0.00314 ( 16) metal coordination : angle 0.46564 ( 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 170 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.342 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: 0.8863 (ttm-80) cc_final: 0.8112 (ttp-170) REVERT: A 136 LYS cc_start: 0.8677 (tttm) cc_final: 0.8462 (tptp) REVERT: B 26 PHE cc_start: 0.8763 (m-10) cc_final: 0.8410 (m-10) REVERT: B 35 GLU cc_start: 0.7852 (tp30) cc_final: 0.6749 (mp0) REVERT: G 20 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8328 (ttp-170) REVERT: G 136 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8396 (tptp) REVERT: H 16 HIS cc_start: 0.7619 (m-70) cc_final: 0.7247 (m90) REVERT: H 35 GLU cc_start: 0.7813 (tp30) cc_final: 0.6763 (mp0) outliers start: 17 outliers final: 12 residues processed: 160 average time/residue: 0.5819 time to fit residues: 100.3227 Evaluate side-chains 159 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 20 ARG Chi-restraints excluded: chain G residue 136 LYS Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain I residue 213 LEU 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: 0.9990 chunk 84 optimal weight: 0.0030 chunk 57 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 14 optimal weight: 0.1980 chunk 104 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 117 ASN B 168 GLN H 117 ASN H 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.137213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.103322 restraints weight = 11921.716| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.53 r_work: 0.2953 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11176 Z= 0.118 Angle : 0.448 6.328 15378 Z= 0.256 Chirality : 0.040 0.146 1708 Planarity : 0.003 0.037 1676 Dihedral : 21.451 62.066 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.74 % Allowed : 17.08 % Favored : 81.19 % 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 aren not related in a simple way. whole: 0.81 (0.25), residues: 1130 helix: 1.87 (0.23), residues: 500 sheet: 0.29 (0.35), residues: 194 loop : -0.93 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 262 TYR 0.010 0.001 TYR B 83 PHE 0.020 0.001 PHE H 26 TRP 0.023 0.001 TRP H 131 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00264 (11160) covalent geometry : angle 0.44843 (15374) hydrogen bonds : bond 0.02902 ( 576) hydrogen bonds : angle 4.17119 ( 1568) metal coordination : bond 0.00269 ( 16) metal coordination : angle 0.42572 ( 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 163 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.425 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: 0.8789 (ttm-80) cc_final: 0.7958 (ttp-170) REVERT: A 136 LYS cc_start: 0.8615 (tttm) cc_final: 0.8346 (tptp) REVERT: B 35 GLU cc_start: 0.7815 (tp30) cc_final: 0.6671 (mp0) REVERT: G 20 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8259 (ttp-170) REVERT: G 136 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8303 (tptp) REVERT: H 16 HIS cc_start: 0.7419 (m-70) cc_final: 0.7047 (m90) REVERT: H 35 GLU cc_start: 0.7768 (tp30) cc_final: 0.6637 (mp0) outliers start: 17 outliers final: 11 residues processed: 152 average time/residue: 0.6508 time to fit residues: 106.5024 Evaluate side-chains 157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 20 ARG Chi-restraints excluded: chain G residue 136 LYS Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 117 ASN Chi-restraints excluded: chain I residue 213 LEU 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: 4.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 94 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 148 GLN A 155 ASN B 117 ASN B 168 GLN H 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.137910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.103303 restraints weight = 13485.437| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.65 r_work: 0.2979 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11176 Z= 0.157 Angle : 0.777 59.199 15378 Z= 0.479 Chirality : 0.041 0.211 1708 Planarity : 0.003 0.040 1676 Dihedral : 21.454 62.066 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.90 % Rotamer: Outliers : 1.43 % Allowed : 18.00 % Favored : 80.57 % Cbeta Deviations : 0.09 % 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 aren not related in a simple way. whole: 0.83 (0.25), residues: 1130 helix: 1.88 (0.23), residues: 500 sheet: 0.30 (0.35), residues: 194 loop : -0.91 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 262 TYR 0.010 0.001 TYR B 83 PHE 0.011 0.001 PHE H 26 TRP 0.021 0.001 TRP H 131 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00324 (11160) covalent geometry : angle 0.77701 (15374) hydrogen bonds : bond 0.02909 ( 576) hydrogen bonds : angle 4.17017 ( 1568) metal coordination : bond 0.00279 ( 16) metal coordination : angle 0.42647 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4411.31 seconds wall clock time: 75 minutes 53.10 seconds (4553.10 seconds total)