Starting phenix.real_space_refine on Tue Jul 29 12:52:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9m_45364/07_2025/9c9m_45364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9m_45364/07_2025/9c9m_45364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c9m_45364/07_2025/9c9m_45364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9m_45364/07_2025/9c9m_45364.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9m_45364/07_2025/9c9m_45364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9m_45364/07_2025/9c9m_45364.cif" } resolution = 2.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 2 6.06 5 P 72 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 7046 2.51 5 N 2040 2.21 5 O 2299 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11503 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2049 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Chain: "B" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain breaks: 3 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: "I" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2049 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Chain: "K" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain breaks: 3 Chain: "M" 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: "N" 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: "O" 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: "L" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 572 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "C" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 572 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DLU': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DLU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "O" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 319 SG CYS A 40 42.542 92.168 31.182 1.00 17.47 S ATOM 342 SG CYS A 43 45.478 90.410 32.452 1.00 19.39 S ATOM 5425 SG CYS I 40 60.382 38.974 31.194 1.00 17.38 S ATOM 5448 SG CYS I 43 57.434 40.738 32.449 1.00 19.60 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DA F 21 " occ=0.58 ... (40 atoms not shown) pdb=" C4 B DA F 21 " occ=0.42 residue: pdb=" P A DA O 21 " occ=0.56 ... (40 atoms not shown) pdb=" C4 B DA O 21 " occ=0.44 Time building chain proxies: 9.38, per 1000 atoms: 0.82 Number of scatterers: 11503 At special positions: 0 Unit cell: (103.75, 132.8, 87.15, 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 2 29.99 S 36 16.00 P 72 15.00 Mg 4 11.99 F 4 9.00 O 2299 8.00 N 2040 7.00 C 7046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 43 " pdb=" ZN I 303 " pdb="ZN ZN I 303 " - pdb=" ND1 HIS I 16 " pdb="ZN ZN I 303 " - pdb=" NE2 HIS I 12 " pdb="ZN ZN I 303 " - pdb=" SG CYS I 40 " pdb="ZN ZN I 303 " - pdb=" SG CYS I 43 " Number of angles added : 4 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 12 sheets defined 47.7% alpha, 22.3% beta 32 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 4.43 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 removed outlier: 3.668A pdb=" N ASP A 6 " --> pdb=" O LEU A 2 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 7 " --> pdb=" O ASP A 3 " (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 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 166 Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 171 through 186 Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.517A pdb=" N TYR A 194 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 221 Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.777A pdb=" N CYS B 40 " --> pdb=" O ILE B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 108 Processing helix chain 'B' and resid 123 through 133 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 187 removed outlier: 3.910A pdb=" N ARG B 187 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 221 Processing helix chain 'I' and resid 2 through 16 Processing helix chain 'I' and resid 18 through 26 Processing helix chain 'I' and resid 29 through 39 Processing helix chain 'I' and resid 40 through 44 Processing helix chain 'I' and resid 93 through 108 Processing helix chain 'I' and resid 118 through 123 Processing helix chain 'I' and resid 123 through 133 Processing helix chain 'I' and resid 144 through 147 Processing helix chain 'I' and resid 148 through 165 Processing helix chain 'I' and resid 166 through 169 removed outlier: 3.670A pdb=" N ALA I 169 " --> pdb=" O ARG I 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 166 through 169' Processing helix chain 'I' and resid 171 through 186 Processing helix chain 'I' and resid 190 through 194 removed outlier: 3.617A pdb=" N TYR I 194 " --> pdb=" O ILE I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 221 Processing helix chain 'K' and resid 4 through 16 Processing helix chain 'K' and resid 18 through 27 Processing helix chain 'K' and resid 29 through 40 removed outlier: 3.799A pdb=" N CYS K 40 " --> pdb=" O ILE K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 108 Processing helix chain 'K' and resid 118 through 123 Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 150 through 166 Processing helix chain 'K' and resid 167 through 169 No H-bonds generated for 'chain 'K' and resid 167 through 169' Processing helix chain 'K' and resid 171 through 186 Processing helix chain 'K' and resid 195 through 222 removed outlier: 3.913A pdb=" N ASN K 222 " --> pdb=" O THR K 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 223 removed outlier: 3.869A pdb=" N PHE L 223 " --> pdb=" O LYS L 219 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 277 Processing helix chain 'C' and resid 213 through 223 removed outlier: 3.863A pdb=" N PHE C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 277 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 3.565A pdb=" N TYR A 83 " --> pdb=" O HIS A 78 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 72 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP A 61 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL A 113 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 256 through 261 removed outlier: 6.999A pdb=" N ALA A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS A 244 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL A 250 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 89 removed outlier: 4.273A pdb=" N VAL B 72 " --> pdb=" O ILE B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 257 through 261 removed outlier: 6.260A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 241 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHE B 223 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 256 through 261 removed outlier: 6.818A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL D 225 " --> pdb=" O PRO D 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 83 through 89 removed outlier: 3.564A pdb=" N TYR I 83 " --> pdb=" O HIS I 78 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL I 72 " --> pdb=" O ILE I 89 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TRP I 61 " --> pdb=" O HIS I 114 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL I 113 " --> pdb=" O GLU I 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 257 through 261 removed outlier: 7.017A pdb=" N ALA I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS I 244 " --> pdb=" O ALA I 248 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL I 250 " --> pdb=" O LEU I 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 84 through 89 removed outlier: 4.298A pdb=" N VAL K 72 " --> pdb=" O ILE K 89 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP K 61 " --> pdb=" O HIS K 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 257 through 261 removed outlier: 6.096A pdb=" N GLN K 252 " --> pdb=" O LEU K 241 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU K 241 " --> pdb=" O GLN K 252 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU K 241 " --> pdb=" O PHE K 223 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE K 223 " --> pdb=" O LEU K 241 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 256 through 261 removed outlier: 6.804A pdb=" N GLN M 252 " --> pdb=" O LEU M 241 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU M 241 " --> pdb=" O GLN M 252 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL M 225 " --> pdb=" O PRO M 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 257 through 261 removed outlier: 6.989A pdb=" N ALA L 248 " --> pdb=" O LYS L 244 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LYS L 244 " --> pdb=" O ALA L 248 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL L 250 " --> pdb=" O LEU L 242 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR L 227 " --> pdb=" O LYS L 236 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL L 225 " --> pdb=" O PRO L 238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 257 through 261 removed outlier: 6.995A pdb=" N ALA C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYS C 244 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C 250 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL C 225 " --> pdb=" O PRO C 238 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2889 1.33 - 1.45: 2452 1.45 - 1.57: 6265 1.57 - 1.69: 142 1.69 - 1.81: 52 Bond restraints: 11800 Sorted by residual: bond pdb=" CAN DLU F 101 " pdb=" CAV DLU F 101 " ideal model delta sigma weight residual 1.505 1.382 0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" CAN DLU O 101 " pdb=" CAV DLU O 101 " ideal model delta sigma weight residual 1.505 1.383 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" CAU DLU F 101 " pdb=" FAG DLU F 101 " ideal model delta sigma weight residual 1.339 1.234 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" CAU DLU O 101 " pdb=" FAG DLU O 101 " ideal model delta sigma weight residual 1.339 1.235 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" CAR DLU F 101 " pdb=" CAX DLU F 101 " ideal model delta sigma weight residual 1.491 1.387 0.104 2.00e-02 2.50e+03 2.68e+01 ... (remaining 11795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 15936 1.84 - 3.69: 256 3.69 - 5.53: 44 5.53 - 7.37: 2 7.37 - 9.21: 2 Bond angle restraints: 16240 Sorted by residual: angle pdb=" NBC DLU O 101 " pdb=" CBB DLU O 101 " pdb=" OAQ DLU O 101 " ideal model delta sigma weight residual 110.33 101.12 9.21 3.00e+00 1.11e-01 9.43e+00 angle pdb=" NBC DLU F 101 " pdb=" CBB DLU F 101 " pdb=" OAQ DLU F 101 " ideal model delta sigma weight residual 110.33 101.13 9.20 3.00e+00 1.11e-01 9.41e+00 angle pdb=" N LYS A 136 " pdb=" CA LYS A 136 " pdb=" C LYS A 136 " ideal model delta sigma weight residual 109.96 104.99 4.97 1.68e+00 3.54e-01 8.75e+00 angle pdb=" N ILE I 135 " pdb=" CA ILE I 135 " pdb=" C ILE I 135 " ideal model delta sigma weight residual 108.17 111.90 -3.73 1.40e+00 5.10e-01 7.10e+00 angle pdb=" C3' DT F 17 " pdb=" C2' DT F 17 " pdb=" C1' DT F 17 " ideal model delta sigma weight residual 101.60 105.23 -3.63 1.50e+00 4.44e-01 5.84e+00 ... (remaining 16235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.49: 6186 25.49 - 50.99: 573 50.99 - 76.48: 162 76.48 - 101.98: 19 101.98 - 127.47: 2 Dihedral angle restraints: 6942 sinusoidal: 3390 harmonic: 3552 Sorted by residual: dihedral pdb=" CA TYR A 194 " pdb=" C TYR A 194 " pdb=" N SER A 195 " pdb=" CA SER A 195 " ideal model delta harmonic sigma weight residual 180.00 154.69 25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA TYR I 194 " pdb=" C TYR I 194 " pdb=" N SER I 195 " pdb=" CA SER I 195 " ideal model delta harmonic sigma weight residual 180.00 154.97 25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CAM DLU O 101 " pdb=" CAL DLU O 101 " pdb=" OAQ DLU O 101 " pdb=" CBB DLU O 101 " ideal model delta sinusoidal sigma weight residual -69.82 57.65 -127.47 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 6939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1050 0.030 - 0.060: 406 0.060 - 0.089: 189 0.089 - 0.119: 119 0.119 - 0.149: 16 Chirality restraints: 1780 Sorted by residual: chirality pdb=" CA ILE I 141 " pdb=" N ILE I 141 " pdb=" C ILE I 141 " pdb=" CB ILE I 141 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE A 141 " pdb=" N ILE A 141 " pdb=" C ILE A 141 " pdb=" CB ILE A 141 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA LYS A 136 " pdb=" N LYS A 136 " pdb=" C LYS A 136 " pdb=" CB LYS A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 1777 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 155 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C ASN A 155 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN A 155 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 156 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 260 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO B 261 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 18 " -0.023 2.00e-02 2.50e+03 1.03e-02 3.19e+00 pdb=" N9 DG N 18 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DG N 18 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG N 18 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG N 18 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG N 18 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG N 18 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG N 18 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG N 18 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG N 18 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DG N 18 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG N 18 " 0.003 2.00e-02 2.50e+03 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 115 2.56 - 3.14: 8983 3.14 - 3.73: 18885 3.73 - 4.31: 26809 4.31 - 4.90: 41711 Nonbonded interactions: 96503 Sorted by model distance: nonbonded pdb="MG MG A 301 " pdb=" O HOH A 408 " model vdw 1.971 2.170 nonbonded pdb="MG MG I 301 " pdb=" O HOH I 407 " model vdw 1.972 2.170 nonbonded pdb="MG MG A 301 " pdb=" O HOH A 405 " model vdw 1.978 2.170 nonbonded pdb="MG MG I 301 " pdb=" O HOH I 405 " model vdw 1.978 2.170 nonbonded pdb=" OD2 ASP A 64 " pdb="MG MG A 302 " model vdw 2.025 2.170 ... (remaining 96498 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' and (resid 2 through 44 or resid 57 through 140 or resid 150 through \ 268)) selection = (chain 'B' and (resid 2 through 228 or resid 236 through 268)) selection = (chain 'I' and (resid 2 through 44 or resid 57 through 140 or resid 150 through \ 268)) selection = (chain 'K' and (resid 2 through 228 or resid 236 through 268)) } ncs_group { reference = chain 'C' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'N' } ncs_group { reference = (chain 'F' and (resid 5 through 20 or resid 101)) selection = (chain 'O' and (resid 5 through 20 or resid 101)) } 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=0.42 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: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 36.960 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:14.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 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 : 0.005 0.123 11808 Z= 0.232 Angle : 0.596 12.175 16244 Z= 0.317 Chirality : 0.044 0.149 1780 Planarity : 0.004 0.050 1802 Dihedral : 19.979 127.472 4650 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.19 % Allowed : 12.96 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1208 helix: 1.80 (0.22), residues: 526 sheet: 1.17 (0.30), residues: 282 loop : -0.74 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 243 HIS 0.004 0.001 HIS I 51 PHE 0.011 0.001 PHE I 181 TYR 0.016 0.001 TYR I 99 ARG 0.003 0.000 ARG K 107 Details of bonding type rmsd hydrogen bonds : bond 0.11710 ( 636) hydrogen bonds : angle 5.77419 ( 1747) metal coordination : bond 0.06861 ( 8) metal coordination : angle 9.62372 ( 4) covalent geometry : bond 0.00465 (11800) covalent geometry : angle 0.57669 (16240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 253 ASP cc_start: 0.6045 (t70) cc_final: 0.5461 (t0) REVERT: K 253 ASP cc_start: 0.6073 (t0) cc_final: 0.5708 (t0) outliers start: 2 outliers final: 1 residues processed: 224 average time/residue: 1.2782 time to fit residues: 308.5183 Evaluate side-chains 125 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 B 27 ASN B 117 ASN B 222 ASN D 254 ASN I 114 HIS I 148 GLN K 216 GLN L 274 GLN C 274 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.136804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.093445 restraints weight = 20089.001| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.93 r_work: 0.3261 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11808 Z= 0.165 Angle : 0.605 9.095 16244 Z= 0.328 Chirality : 0.044 0.159 1780 Planarity : 0.004 0.045 1802 Dihedral : 21.093 61.993 2222 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.26 % Allowed : 15.74 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1208 helix: 1.89 (0.22), residues: 534 sheet: 1.38 (0.31), residues: 286 loop : -0.70 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 19 HIS 0.008 0.001 HIS B 12 PHE 0.014 0.001 PHE K 223 TYR 0.014 0.002 TYR A 83 ARG 0.008 0.001 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 636) hydrogen bonds : angle 4.59155 ( 1747) metal coordination : bond 0.01043 ( 8) metal coordination : angle 6.49612 ( 4) covalent geometry : bond 0.00365 (11800) covalent geometry : angle 0.59618 (16240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 1.582 Fit side-chains revert: symmetry clash REVERT: D 240 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7796 (tptp) REVERT: K 22 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.4975 (ptp) REVERT: L 224 ARG cc_start: 0.7808 (mtt-85) cc_final: 0.7550 (mmm-85) REVERT: C 224 ARG cc_start: 0.7886 (mtt-85) cc_final: 0.7627 (mmm-85) outliers start: 34 outliers final: 6 residues processed: 174 average time/residue: 2.2728 time to fit residues: 422.5072 Evaluate side-chains 141 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain K residue 22 MET Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN B 222 ASN D 254 ASN K 222 ASN L 214 GLN C 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.132404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088069 restraints weight = 21533.985| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.00 r_work: 0.3149 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11808 Z= 0.161 Angle : 0.547 8.757 16244 Z= 0.303 Chirality : 0.043 0.140 1780 Planarity : 0.004 0.043 1802 Dihedral : 20.994 62.244 2220 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.98 % Allowed : 16.41 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1208 helix: 2.06 (0.21), residues: 536 sheet: 1.21 (0.32), residues: 266 loop : -0.43 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 19 HIS 0.005 0.001 HIS A 114 PHE 0.010 0.002 PHE I 100 TYR 0.014 0.002 TYR B 83 ARG 0.008 0.001 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 636) hydrogen bonds : angle 4.56012 ( 1747) metal coordination : bond 0.01681 ( 8) metal coordination : angle 4.79220 ( 4) covalent geometry : bond 0.00359 (11800) covalent geometry : angle 0.54144 (16240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.260 Fit side-chains REVERT: A 9 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: B 188 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6901 (mmtp) REVERT: D 240 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7833 (tptp) REVERT: I 9 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7962 (mt0) REVERT: K 188 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6773 (mmtp) REVERT: L 224 ARG cc_start: 0.7842 (mtt-85) cc_final: 0.7582 (mmm-85) REVERT: C 224 ARG cc_start: 0.7914 (mtt-85) cc_final: 0.7645 (mmm-85) outliers start: 31 outliers final: 6 residues processed: 154 average time/residue: 1.4969 time to fit residues: 247.0857 Evaluate side-chains 135 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN C 216 GLN C 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.133365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.088647 restraints weight = 23269.837| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.07 r_work: 0.3135 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11808 Z= 0.137 Angle : 0.523 8.516 16244 Z= 0.288 Chirality : 0.042 0.143 1780 Planarity : 0.004 0.043 1802 Dihedral : 20.978 63.315 2220 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.78 % Allowed : 15.83 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1208 helix: 2.19 (0.21), residues: 534 sheet: 1.29 (0.31), residues: 282 loop : -0.62 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 19 HIS 0.005 0.001 HIS B 183 PHE 0.016 0.001 PHE B 26 TYR 0.012 0.001 TYR A 83 ARG 0.006 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 636) hydrogen bonds : angle 4.48500 ( 1747) metal coordination : bond 0.01152 ( 8) metal coordination : angle 4.68492 ( 4) covalent geometry : bond 0.00305 (11800) covalent geometry : angle 0.51777 (16240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8052 (mt0) REVERT: D 240 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7894 (tptp) REVERT: I 9 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.8039 (mt0) REVERT: K 27 ASN cc_start: 0.8878 (t0) cc_final: 0.8644 (t0) REVERT: K 188 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6779 (mmtp) REVERT: L 224 ARG cc_start: 0.7867 (mtt-85) cc_final: 0.7582 (mmm-85) REVERT: C 224 ARG cc_start: 0.7905 (mtt-85) cc_final: 0.7634 (mmm-85) outliers start: 29 outliers final: 13 residues processed: 147 average time/residue: 1.8264 time to fit residues: 286.5193 Evaluate side-chains 139 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN L 221 GLN C 216 GLN C 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.130918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.086804 restraints weight = 17154.303| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.82 r_work: 0.3079 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11808 Z= 0.194 Angle : 0.566 7.244 16244 Z= 0.310 Chirality : 0.044 0.144 1780 Planarity : 0.004 0.044 1802 Dihedral : 21.042 63.834 2220 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.98 % Allowed : 15.93 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1208 helix: 2.07 (0.21), residues: 534 sheet: 1.20 (0.31), residues: 282 loop : -0.65 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 19 HIS 0.006 0.001 HIS I 16 PHE 0.016 0.002 PHE B 26 TYR 0.014 0.002 TYR A 83 ARG 0.004 0.000 ARG D 263 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 636) hydrogen bonds : angle 4.61339 ( 1747) metal coordination : bond 0.01524 ( 8) metal coordination : angle 4.66404 ( 4) covalent geometry : bond 0.00441 (11800) covalent geometry : angle 0.56095 (16240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.267 Fit side-chains REVERT: A 9 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: B 27 ASN cc_start: 0.8920 (t0) cc_final: 0.8600 (t0) REVERT: B 188 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6849 (mmtp) REVERT: D 240 LYS cc_start: 0.8214 (mmmt) cc_final: 0.7793 (tptp) REVERT: D 258 LYS cc_start: 0.8667 (mttt) cc_final: 0.8464 (mttm) REVERT: I 9 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8025 (mt0) REVERT: K 27 ASN cc_start: 0.8877 (t0) cc_final: 0.8623 (t0) REVERT: K 188 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6804 (mmtp) REVERT: L 224 ARG cc_start: 0.7833 (mtt-85) cc_final: 0.7535 (mmm-85) REVERT: C 224 ARG cc_start: 0.7865 (mtt-85) cc_final: 0.7576 (mmm-85) outliers start: 31 outliers final: 13 residues processed: 147 average time/residue: 2.1081 time to fit residues: 331.7031 Evaluate side-chains 139 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 214 GLN L 221 GLN C 216 GLN C 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.132638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088452 restraints weight = 22134.905| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.02 r_work: 0.3135 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11808 Z= 0.130 Angle : 0.512 7.616 16244 Z= 0.284 Chirality : 0.042 0.149 1780 Planarity : 0.003 0.042 1802 Dihedral : 20.930 64.849 2220 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.78 % Allowed : 16.79 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1208 helix: 2.21 (0.22), residues: 534 sheet: 1.18 (0.31), residues: 282 loop : -0.62 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP K 19 HIS 0.004 0.001 HIS A 12 PHE 0.019 0.001 PHE B 26 TYR 0.013 0.001 TYR A 83 ARG 0.004 0.000 ARG L 224 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 636) hydrogen bonds : angle 4.47904 ( 1747) metal coordination : bond 0.01250 ( 8) metal coordination : angle 4.51560 ( 4) covalent geometry : bond 0.00288 (11800) covalent geometry : angle 0.50743 (16240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: A 156 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8706 (tmmm) REVERT: B 27 ASN cc_start: 0.8848 (t0) cc_final: 0.8516 (t0) REVERT: D 240 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8072 (tptp) REVERT: I 9 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: K 27 ASN cc_start: 0.8780 (t0) cc_final: 0.8519 (t0) REVERT: L 224 ARG cc_start: 0.7903 (mtt-85) cc_final: 0.7613 (mmm-85) REVERT: C 224 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.7696 (mmm-85) outliers start: 29 outliers final: 17 residues processed: 144 average time/residue: 1.4757 time to fit residues: 228.1748 Evaluate side-chains 146 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 100 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.131945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.087594 restraints weight = 21755.614| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.02 r_work: 0.3119 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11808 Z= 0.146 Angle : 0.525 7.568 16244 Z= 0.290 Chirality : 0.043 0.142 1780 Planarity : 0.004 0.042 1802 Dihedral : 20.964 64.092 2220 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.50 % Allowed : 16.89 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1208 helix: 2.19 (0.22), residues: 534 sheet: 1.19 (0.30), residues: 282 loop : -0.60 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP K 19 HIS 0.004 0.001 HIS A 16 PHE 0.020 0.001 PHE B 26 TYR 0.013 0.001 TYR A 83 ARG 0.006 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 636) hydrogen bonds : angle 4.48414 ( 1747) metal coordination : bond 0.01232 ( 8) metal coordination : angle 4.26296 ( 4) covalent geometry : bond 0.00328 (11800) covalent geometry : angle 0.52091 (16240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8108 (mt0) REVERT: A 156 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8804 (tmmm) REVERT: B 27 ASN cc_start: 0.8813 (t0) cc_final: 0.8495 (t0) REVERT: D 240 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8092 (tptp) REVERT: I 9 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8091 (mt0) REVERT: K 26 PHE cc_start: 0.7834 (m-80) cc_final: 0.7606 (m-80) REVERT: K 27 ASN cc_start: 0.8744 (t0) cc_final: 0.8479 (t0) REVERT: L 224 ARG cc_start: 0.7883 (mtt-85) cc_final: 0.7582 (mmm-85) REVERT: C 224 ARG cc_start: 0.7923 (mtt-85) cc_final: 0.7641 (mmm-85) outliers start: 26 outliers final: 17 residues processed: 141 average time/residue: 1.4534 time to fit residues: 219.4643 Evaluate side-chains 143 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 94 optimal weight: 0.0470 chunk 57 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.131283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.086140 restraints weight = 29625.970| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.30 r_work: 0.3086 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11808 Z= 0.161 Angle : 0.538 7.607 16244 Z= 0.297 Chirality : 0.043 0.142 1780 Planarity : 0.004 0.043 1802 Dihedral : 21.008 64.632 2220 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.40 % Allowed : 17.08 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1208 helix: 2.14 (0.21), residues: 534 sheet: 1.18 (0.31), residues: 282 loop : -0.58 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP K 19 HIS 0.005 0.001 HIS A 16 PHE 0.024 0.002 PHE B 26 TYR 0.014 0.001 TYR A 83 ARG 0.008 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 636) hydrogen bonds : angle 4.53347 ( 1747) metal coordination : bond 0.01406 ( 8) metal coordination : angle 4.27554 ( 4) covalent geometry : bond 0.00365 (11800) covalent geometry : angle 0.53379 (16240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.164 Fit side-chains REVERT: A 9 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: A 156 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8826 (tmmm) REVERT: B 27 ASN cc_start: 0.8696 (t0) cc_final: 0.8414 (t0) REVERT: D 240 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8097 (tptm) REVERT: I 9 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8110 (mt0) REVERT: K 26 PHE cc_start: 0.7763 (m-80) cc_final: 0.7518 (m-80) REVERT: K 27 ASN cc_start: 0.8738 (t0) cc_final: 0.8467 (t0) REVERT: L 224 ARG cc_start: 0.7943 (mtt-85) cc_final: 0.7648 (mmm-85) REVERT: C 224 ARG cc_start: 0.7956 (mtt-85) cc_final: 0.7672 (mmm-85) outliers start: 25 outliers final: 16 residues processed: 137 average time/residue: 1.4294 time to fit residues: 209.7804 Evaluate side-chains 136 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.130287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.084914 restraints weight = 32986.140| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.41 r_work: 0.3061 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11808 Z= 0.192 Angle : 0.569 7.536 16244 Z= 0.313 Chirality : 0.044 0.184 1780 Planarity : 0.004 0.043 1802 Dihedral : 21.063 65.129 2220 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.11 % Allowed : 17.75 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1208 helix: 2.08 (0.21), residues: 534 sheet: 1.13 (0.30), residues: 282 loop : -0.61 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP K 19 HIS 0.006 0.001 HIS A 16 PHE 0.029 0.002 PHE B 26 TYR 0.015 0.002 TYR A 83 ARG 0.009 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 636) hydrogen bonds : angle 4.59778 ( 1747) metal coordination : bond 0.01706 ( 8) metal coordination : angle 4.17164 ( 4) covalent geometry : bond 0.00440 (11800) covalent geometry : angle 0.56545 (16240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.163 Fit side-chains REVERT: A 9 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8173 (mt0) REVERT: B 27 ASN cc_start: 0.8642 (t0) cc_final: 0.8373 (t0) REVERT: D 240 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8110 (tptm) REVERT: I 9 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: K 26 PHE cc_start: 0.7748 (m-80) cc_final: 0.7534 (m-80) REVERT: K 27 ASN cc_start: 0.8734 (t0) cc_final: 0.8463 (t0) REVERT: L 224 ARG cc_start: 0.7966 (mtt-85) cc_final: 0.7670 (mmm-85) REVERT: C 224 ARG cc_start: 0.7991 (mtt-85) cc_final: 0.7704 (mmm-85) outliers start: 22 outliers final: 16 residues processed: 136 average time/residue: 1.5074 time to fit residues: 219.3530 Evaluate side-chains 140 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 36 optimal weight: 0.0870 chunk 72 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.132172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087390 restraints weight = 30728.704| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.34 r_work: 0.3084 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11808 Z= 0.131 Angle : 0.527 7.440 16244 Z= 0.292 Chirality : 0.042 0.168 1780 Planarity : 0.004 0.042 1802 Dihedral : 20.970 65.225 2220 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.82 % Allowed : 18.04 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.25), residues: 1208 helix: 2.22 (0.22), residues: 534 sheet: 1.20 (0.31), residues: 282 loop : -0.57 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 19 HIS 0.004 0.001 HIS A 12 PHE 0.030 0.001 PHE B 26 TYR 0.013 0.001 TYR A 83 ARG 0.008 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 636) hydrogen bonds : angle 4.46610 ( 1747) metal coordination : bond 0.01065 ( 8) metal coordination : angle 4.42217 ( 4) covalent geometry : bond 0.00293 (11800) covalent geometry : angle 0.52287 (16240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.338 Fit side-chains REVERT: A 9 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8060 (mt0) REVERT: B 27 ASN cc_start: 0.8557 (t0) cc_final: 0.8306 (t0) REVERT: D 240 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8075 (tptp) REVERT: I 9 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8002 (mt0) REVERT: K 26 PHE cc_start: 0.7699 (m-80) cc_final: 0.7455 (m-80) REVERT: K 27 ASN cc_start: 0.8731 (t0) cc_final: 0.8465 (t0) REVERT: L 224 ARG cc_start: 0.7890 (mtt-85) cc_final: 0.7571 (mmm-85) REVERT: C 224 ARG cc_start: 0.7925 (mtt-85) cc_final: 0.7621 (mmm-85) outliers start: 19 outliers final: 15 residues processed: 133 average time/residue: 1.4738 time to fit residues: 210.6916 Evaluate side-chains 136 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 35 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 84 optimal weight: 0.0570 chunk 71 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.130979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.086236 restraints weight = 24740.051| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.14 r_work: 0.3095 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11808 Z= 0.166 Angle : 0.547 7.473 16244 Z= 0.302 Chirality : 0.043 0.147 1780 Planarity : 0.004 0.043 1802 Dihedral : 21.029 64.831 2220 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.82 % Allowed : 18.23 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.24), residues: 1208 helix: 2.16 (0.22), residues: 534 sheet: 1.18 (0.31), residues: 282 loop : -0.59 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP K 19 HIS 0.005 0.001 HIS A 16 PHE 0.030 0.002 PHE B 26 TYR 0.014 0.002 TYR A 83 ARG 0.009 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 636) hydrogen bonds : angle 4.52482 ( 1747) metal coordination : bond 0.01491 ( 8) metal coordination : angle 4.13424 ( 4) covalent geometry : bond 0.00377 (11800) covalent geometry : angle 0.54296 (16240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23049.97 seconds wall clock time: 410 minutes 45.93 seconds (24645.93 seconds total)