Starting phenix.real_space_refine on Fri Dec 27 21:07:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ul9_42357/12_2024/8ul9_42357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ul9_42357/12_2024/8ul9_42357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ul9_42357/12_2024/8ul9_42357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ul9_42357/12_2024/8ul9_42357.map" model { file = "/net/cci-nas-00/data/ceres_data/8ul9_42357/12_2024/8ul9_42357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ul9_42357/12_2024/8ul9_42357.cif" } resolution = 3.2 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= -0.001 sd= 0.062 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 4 5.21 5 S 42 5.16 5 C 4519 2.51 5 N 959 2.21 5 O 1144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6674 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3144 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 388, 3120 Unusual residues: {'ACE': 1} Classifications: {'peptide': 387, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 17, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 388, 3120 Unusual residues: {'ACE': 1} Classifications: {'peptide': 387, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 17, 'TRANS': 369} bond proxies already assigned to first conformer: 3191 Chain: "B" Number of atoms: 3127 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 388, 3120 Unusual residues: {'ACE': 1} Classifications: {'peptide': 387, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 17, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 388, 3120 Unusual residues: {'ACE': 1} Classifications: {'peptide': 387, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 17, 'TRANS': 369} bond proxies already assigned to first conformer: 3211 Chain: "A" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 200 Unusual residues: {' MG': 2, 'DGA': 1, 'PCW': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 202 Unusual residues: {' MG': 2, 'DGA': 1, 'PCW': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 118 " occ=0.44 ... (18 atoms not shown) pdb=" NE2BHIS A 118 " occ=0.56 Time building chain proxies: 10.80, per 1000 atoms: 1.62 Number of scatterers: 6674 At special positions: 0 Unit cell: (106.92, 96.12, 74.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 6 15.00 Mg 4 11.99 O 1144 8.00 N 959 7.00 C 4519 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: 2.53 Conformation dependent library (CDL) restraints added in 1.5 seconds 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 77.8% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 12 through 16 removed outlier: 3.618A pdb=" N TYR A 16 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 42 removed outlier: 3.754A pdb=" N PHE A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 70 removed outlier: 3.683A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 106 removed outlier: 4.118A pdb=" N PHE A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.616A pdb=" N GLU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 123 " --> pdb=" O CYS A 119 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 137 removed outlier: 4.181A pdb=" N VAL A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 165 removed outlier: 3.535A pdb=" N ILE A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 217 through 248 Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.591A pdb=" N GLU A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 285 Processing helix chain 'A' and resid 286 through 289 removed outlier: 3.600A pdb=" N ILE A 289 " --> pdb=" O PRO A 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 290 through 314 Processing helix chain 'A' and resid 322 through 341 Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 347 through 381 Processing helix chain 'B' and resid 7 through 14 removed outlier: 4.383A pdb=" N GLY B 11 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN B 12 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 13 " --> pdb=" O LEU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 31 removed outlier: 4.520A pdb=" N ASN B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 39 Processing helix chain 'B' and resid 47 through 70 removed outlier: 3.531A pdb=" N VAL B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 106 removed outlier: 4.218A pdb=" N TYR B 82 " --> pdb=" O PRO B 78 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE B 83 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 128 removed outlier: 3.616A pdb=" N GLU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 123 " --> pdb=" O CYS B 119 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 137 removed outlier: 4.303A pdb=" N VAL B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 166 removed outlier: 3.549A pdb=" N ILE B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 193 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 217 through 248 Processing helix chain 'B' and resid 253 through 285 removed outlier: 3.940A pdb=" N THR B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 286 through 289 removed outlier: 3.646A pdb=" N ILE B 289 " --> pdb=" O PRO B 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 286 through 289' Processing helix chain 'B' and resid 290 through 315 Processing helix chain 'B' and resid 322 through 341 Proline residue: B 328 - end of helix Processing helix chain 'B' and resid 345 through 381 removed outlier: 3.642A pdb=" N ILE B 349 " --> pdb=" O GLN B 345 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 204 removed outlier: 3.787A pdb=" N ALA A 204 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 20 through 22 Processing sheet with id=AA3, first strand: chain 'B' and resid 202 through 204 removed outlier: 7.389A pdb=" N VAL B 215 " --> pdb=" O VAL B 203 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1310 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 939 1.31 - 1.43: 2072 1.43 - 1.56: 3777 1.56 - 1.69: 12 1.69 - 1.81: 68 Bond restraints: 6868 Sorted by residual: bond pdb=" C11 PCW A1003 " pdb=" O3 PCW A1003 " ideal model delta sigma weight residual 1.326 1.420 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C11 PCW A1004 " pdb=" O3 PCW A1004 " ideal model delta sigma weight residual 1.326 1.420 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C11 PCW B1004 " pdb=" O3 PCW B1004 " ideal model delta sigma weight residual 1.326 1.419 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C11 PCW A1005 " pdb=" O3 PCW A1005 " ideal model delta sigma weight residual 1.326 1.419 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" C11 PCW B1003 " pdb=" O3 PCW B1003 " ideal model delta sigma weight residual 1.326 1.419 -0.093 2.00e-02 2.50e+03 2.15e+01 ... (remaining 6863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.10: 9193 5.10 - 10.21: 65 10.21 - 15.31: 15 15.31 - 20.42: 3 20.42 - 25.52: 6 Bond angle restraints: 9282 Sorted by residual: angle pdb=" C19 PCW B1003 " pdb=" C20 PCW B1003 " pdb=" C21 PCW B1003 " ideal model delta sigma weight residual 127.82 153.34 -25.52 3.00e+00 1.11e-01 7.24e+01 angle pdb=" C19 PCW B1005 " pdb=" C20 PCW B1005 " pdb=" C21 PCW B1005 " ideal model delta sigma weight residual 127.82 152.95 -25.13 3.00e+00 1.11e-01 7.02e+01 angle pdb=" C19 PCW A1004 " pdb=" C20 PCW A1004 " pdb=" C21 PCW A1004 " ideal model delta sigma weight residual 127.82 152.71 -24.89 3.00e+00 1.11e-01 6.88e+01 angle pdb=" C19 PCW B1004 " pdb=" C20 PCW B1004 " pdb=" C21 PCW B1004 " ideal model delta sigma weight residual 127.82 152.34 -24.52 3.00e+00 1.11e-01 6.68e+01 angle pdb=" C19 PCW A1005 " pdb=" C20 PCW A1005 " pdb=" C21 PCW A1005 " ideal model delta sigma weight residual 127.82 152.27 -24.45 3.00e+00 1.11e-01 6.64e+01 ... (remaining 9277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 3865 35.89 - 71.79: 151 71.79 - 107.68: 5 107.68 - 143.58: 3 143.58 - 179.47: 7 Dihedral angle restraints: 4031 sinusoidal: 1737 harmonic: 2294 Sorted by residual: dihedral pdb=" CH3 ACE B 1 " pdb=" C ACE B 1 " pdb=" N GLY B 2 " pdb=" CA GLY B 2 " ideal model delta sinusoidal sigma weight residual -180.00 -0.53 -179.47 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE A 1 " pdb=" C ACE A 1 " pdb=" N GLY A 2 " pdb=" CA GLY A 2 " ideal model delta sinusoidal sigma weight residual -180.00 -0.64 -179.36 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" N PCW A1004 " pdb=" C4 PCW A1004 " pdb=" C5 PCW A1004 " pdb=" O4P PCW A1004 " ideal model delta sinusoidal sigma weight residual 293.34 126.41 166.93 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 4028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 773 0.047 - 0.094: 192 0.094 - 0.140: 34 0.140 - 0.187: 0 0.187 - 0.234: 5 Chirality restraints: 1004 Sorted by residual: chirality pdb=" C2 PCW A1003 " pdb=" C1 PCW A1003 " pdb=" C3 PCW A1003 " pdb=" O2 PCW A1003 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C2 PCW B1005 " pdb=" C1 PCW B1005 " pdb=" C3 PCW B1005 " pdb=" O2 PCW B1005 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C2 PCW A1005 " pdb=" C1 PCW A1005 " pdb=" C3 PCW A1005 " pdb=" O2 PCW A1005 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1001 not shown) Planarity restraints: 1113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 347 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.42e+00 pdb=" C GLY A 347 " -0.027 2.00e-02 2.50e+03 pdb=" O GLY A 347 " 0.010 2.00e-02 2.50e+03 pdb=" N SER A 348 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 175 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO B 176 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 176 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 176 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 269 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO B 270 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.018 5.00e-02 4.00e+02 ... (remaining 1110 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 57 2.60 - 3.17: 5721 3.17 - 3.75: 10261 3.75 - 4.32: 14183 4.32 - 4.90: 24343 Nonbonded interactions: 54565 Sorted by model distance: nonbonded pdb=" OD1 ASP A 121 " pdb="MG MG A1002 " model vdw 2.024 2.170 nonbonded pdb=" OD1 ASP B 121 " pdb="MG MG B1002 " model vdw 2.029 2.170 nonbonded pdb=" OD1 ASP B 117 " pdb="MG MG B1002 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP A 96 " pdb="MG MG A1002 " model vdw 2.204 2.170 nonbonded pdb=" OD2 ASP B 117 " pdb="MG MG B1001 " model vdw 2.209 2.170 ... (remaining 54560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 117 or resid 119 throug \ h 271 or resid 273 through 388 or resid 1001 through 1007)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 117 or resid 119 throug \ h 271 or resid 273 through 388 or resid 1001 through 1004 or (resid 1005 and (na \ me N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or n \ ame C16 or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 o \ r name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or \ name C42 or name C43 or name C44 or name C45 or name C46 or name C5 or name C6 o \ r name C7 or name C8 or name O11 or name O1P or name O2 or name O2P or name O3 o \ r name O31 or name O3P or name O4P or name P )) or resid 1007)) } 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=0.19 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: 2.550 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.340 Process input model: 28.480 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.008 0.094 6868 Z= 0.532 Angle : 1.290 25.522 9282 Z= 0.478 Chirality : 0.042 0.234 1004 Planarity : 0.004 0.037 1113 Dihedral : 19.116 179.471 2563 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.33 % Allowed : 5.23 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.31), residues: 776 helix: 2.42 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -1.46 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 160 HIS 0.004 0.001 HIS A 164 PHE 0.013 0.001 PHE A 275 TYR 0.015 0.001 TYR A 274 ARG 0.001 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 38 PHE cc_start: 0.5544 (OUTLIER) cc_final: 0.5280 (t80) REVERT: A 92 TYR cc_start: 0.7852 (t80) cc_final: 0.7650 (t80) REVERT: A 369 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8006 (tp) REVERT: A 375 ASP cc_start: 0.7427 (t0) cc_final: 0.7019 (t0) REVERT: B 92 TYR cc_start: 0.7926 (t80) cc_final: 0.7715 (t80) REVERT: B 224 PHE cc_start: 0.8090 (t80) cc_final: 0.7677 (t80) REVERT: B 290 SER cc_start: 0.8751 (t) cc_final: 0.8431 (p) REVERT: B 320 MET cc_start: 0.8872 (tpp) cc_final: 0.8352 (mmt) outliers start: 15 outliers final: 6 residues processed: 115 average time/residue: 0.1614 time to fit residues: 27.5835 Evaluate side-chains 97 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 124 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6868 Z= 0.188 Angle : 0.497 6.728 9282 Z= 0.257 Chirality : 0.040 0.127 1004 Planarity : 0.004 0.037 1113 Dihedral : 21.622 179.744 1206 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 1.45 % Allowed : 8.72 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.30), residues: 776 helix: 2.29 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -1.42 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 160 HIS 0.004 0.001 HIS A 164 PHE 0.012 0.001 PHE A 61 TYR 0.010 0.001 TYR A 274 ARG 0.003 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 290 SER cc_start: 0.8586 (t) cc_final: 0.8251 (p) REVERT: A 369 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7582 (tp) REVERT: B 70 ASP cc_start: 0.8103 (t0) cc_final: 0.7901 (t0) REVERT: B 92 TYR cc_start: 0.7879 (t80) cc_final: 0.7670 (t80) REVERT: B 95 PHE cc_start: 0.7255 (m-80) cc_final: 0.7041 (m-80) REVERT: B 99 ASP cc_start: 0.6459 (OUTLIER) cc_final: 0.6083 (p0) REVERT: B 224 PHE cc_start: 0.8115 (t80) cc_final: 0.7736 (t80) REVERT: B 290 SER cc_start: 0.8663 (t) cc_final: 0.8332 (p) REVERT: B 320 MET cc_start: 0.8816 (tpp) cc_final: 0.8266 (mmt) outliers start: 9 outliers final: 5 residues processed: 95 average time/residue: 0.1492 time to fit residues: 20.8454 Evaluate side-chains 97 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 101 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6868 Z= 0.236 Angle : 0.509 6.434 9282 Z= 0.261 Chirality : 0.040 0.137 1004 Planarity : 0.004 0.036 1113 Dihedral : 19.984 179.650 1200 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 2.18 % Allowed : 9.59 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.31), residues: 776 helix: 2.38 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -1.48 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 160 HIS 0.004 0.001 HIS A 164 PHE 0.014 0.001 PHE A 275 TYR 0.015 0.001 TYR B 156 ARG 0.004 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 196 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8247 (mm110) REVERT: A 290 SER cc_start: 0.8608 (t) cc_final: 0.8266 (p) REVERT: B 70 ASP cc_start: 0.8250 (t0) cc_final: 0.8016 (t0) REVERT: B 92 TYR cc_start: 0.7884 (t80) cc_final: 0.7677 (t80) REVERT: B 224 PHE cc_start: 0.8107 (t80) cc_final: 0.7721 (t80) REVERT: B 290 SER cc_start: 0.8660 (t) cc_final: 0.8332 (p) REVERT: B 320 MET cc_start: 0.8802 (tpp) cc_final: 0.8156 (mmt) outliers start: 14 outliers final: 13 residues processed: 100 average time/residue: 0.1340 time to fit residues: 19.5132 Evaluate side-chains 97 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 135 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6868 Z= 0.207 Angle : 0.489 6.592 9282 Z= 0.252 Chirality : 0.040 0.142 1004 Planarity : 0.004 0.035 1113 Dihedral : 18.919 179.766 1200 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.97 % Rotamer: Outliers : 2.47 % Allowed : 10.17 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.10 (0.31), residues: 776 helix: 2.45 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -1.53 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 160 HIS 0.004 0.001 HIS A 164 PHE 0.012 0.001 PHE A 275 TYR 0.014 0.001 TYR B 156 ARG 0.004 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 290 SER cc_start: 0.8587 (t) cc_final: 0.8265 (p) REVERT: B 70 ASP cc_start: 0.8203 (t0) cc_final: 0.7998 (t0) REVERT: B 224 PHE cc_start: 0.8155 (t80) cc_final: 0.7720 (t80) REVERT: B 290 SER cc_start: 0.8644 (t) cc_final: 0.8319 (p) REVERT: B 320 MET cc_start: 0.8783 (tpp) cc_final: 0.8396 (mmt) outliers start: 16 outliers final: 10 residues processed: 97 average time/residue: 0.1459 time to fit residues: 20.6780 Evaluate side-chains 95 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 343 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 0.0970 chunk 62 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6868 Z= 0.209 Angle : 0.492 6.975 9282 Z= 0.253 Chirality : 0.040 0.143 1004 Planarity : 0.004 0.035 1113 Dihedral : 18.102 179.713 1196 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 2.33 % Allowed : 10.32 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.08 (0.31), residues: 776 helix: 2.44 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -1.55 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 160 HIS 0.004 0.001 HIS A 164 PHE 0.013 0.001 PHE A 275 TYR 0.013 0.001 TYR B 156 ARG 0.002 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 290 SER cc_start: 0.8591 (t) cc_final: 0.8271 (p) REVERT: B 70 ASP cc_start: 0.8246 (t0) cc_final: 0.8016 (t0) REVERT: B 99 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6531 (p0) REVERT: B 224 PHE cc_start: 0.8133 (t80) cc_final: 0.7703 (t80) REVERT: B 290 SER cc_start: 0.8626 (t) cc_final: 0.8310 (p) REVERT: B 320 MET cc_start: 0.8755 (tpp) cc_final: 0.8371 (mmt) outliers start: 15 outliers final: 12 residues processed: 99 average time/residue: 0.1442 time to fit residues: 20.6802 Evaluate side-chains 97 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 343 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 38 optimal weight: 0.0670 chunk 70 optimal weight: 0.0470 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6868 Z= 0.166 Angle : 0.459 5.199 9282 Z= 0.240 Chirality : 0.039 0.145 1004 Planarity : 0.004 0.034 1113 Dihedral : 17.306 179.688 1196 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 2.03 % Allowed : 11.34 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.24 (0.31), residues: 776 helix: 2.57 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -1.53 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 160 HIS 0.003 0.001 HIS A 164 PHE 0.012 0.001 PHE B 275 TYR 0.012 0.001 TYR B 156 ARG 0.003 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 290 SER cc_start: 0.8563 (t) cc_final: 0.8262 (p) REVERT: B 99 ASP cc_start: 0.6750 (OUTLIER) cc_final: 0.6437 (p0) REVERT: B 290 SER cc_start: 0.8570 (t) cc_final: 0.8296 (p) REVERT: B 320 MET cc_start: 0.8758 (tpp) cc_final: 0.8352 (mmt) outliers start: 13 outliers final: 9 residues processed: 96 average time/residue: 0.1452 time to fit residues: 20.3395 Evaluate side-chains 90 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 343 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 0.0070 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6868 Z= 0.200 Angle : 0.478 5.274 9282 Z= 0.249 Chirality : 0.040 0.160 1004 Planarity : 0.004 0.034 1113 Dihedral : 17.133 179.657 1194 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.29 % Favored : 95.58 % Rotamer: Outliers : 1.74 % Allowed : 12.21 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.21 (0.31), residues: 776 helix: 2.54 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -1.54 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 160 HIS 0.003 0.001 HIS A 164 PHE 0.013 0.001 PHE A 275 TYR 0.012 0.001 TYR B 156 ARG 0.004 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 290 SER cc_start: 0.8646 (t) cc_final: 0.8348 (p) REVERT: B 69 TYR cc_start: 0.8661 (m-80) cc_final: 0.8252 (m-80) REVERT: B 99 ASP cc_start: 0.6741 (OUTLIER) cc_final: 0.6449 (p0) REVERT: B 224 PHE cc_start: 0.8160 (t80) cc_final: 0.7704 (t80) REVERT: B 290 SER cc_start: 0.8618 (t) cc_final: 0.8306 (p) REVERT: B 320 MET cc_start: 0.8761 (tpp) cc_final: 0.8341 (mmt) outliers start: 11 outliers final: 9 residues processed: 93 average time/residue: 0.1601 time to fit residues: 21.7435 Evaluate side-chains 90 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 343 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 57 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6868 Z= 0.205 Angle : 0.479 5.273 9282 Z= 0.250 Chirality : 0.040 0.143 1004 Planarity : 0.004 0.033 1113 Dihedral : 16.985 179.610 1194 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 1.89 % Allowed : 11.92 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.15 (0.31), residues: 776 helix: 2.49 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -1.57 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 160 HIS 0.003 0.001 HIS A 164 PHE 0.013 0.001 PHE A 275 TYR 0.012 0.001 TYR B 156 ARG 0.004 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 290 SER cc_start: 0.8650 (t) cc_final: 0.8352 (p) REVERT: B 69 TYR cc_start: 0.8626 (m-80) cc_final: 0.8278 (m-80) REVERT: B 99 ASP cc_start: 0.6725 (OUTLIER) cc_final: 0.6438 (p0) REVERT: B 224 PHE cc_start: 0.8165 (t80) cc_final: 0.7719 (t80) REVERT: B 290 SER cc_start: 0.8625 (t) cc_final: 0.8314 (p) REVERT: B 320 MET cc_start: 0.8756 (tpp) cc_final: 0.8317 (mmt) outliers start: 11 outliers final: 10 residues processed: 91 average time/residue: 0.1484 time to fit residues: 19.6502 Evaluate side-chains 88 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 343 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.0070 chunk 44 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6868 Z= 0.191 Angle : 0.471 5.243 9282 Z= 0.246 Chirality : 0.040 0.142 1004 Planarity : 0.004 0.034 1113 Dihedral : 16.796 179.621 1194 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.29 % Favored : 95.58 % Rotamer: Outliers : 2.18 % Allowed : 11.63 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.18 (0.31), residues: 776 helix: 2.52 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -1.56 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 160 HIS 0.003 0.001 HIS A 164 PHE 0.017 0.001 PHE A 95 TYR 0.012 0.001 TYR B 156 ARG 0.006 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 290 SER cc_start: 0.8641 (t) cc_final: 0.8345 (p) REVERT: B 69 TYR cc_start: 0.8608 (m-80) cc_final: 0.8266 (m-80) REVERT: B 99 ASP cc_start: 0.6725 (OUTLIER) cc_final: 0.6438 (p0) REVERT: B 224 PHE cc_start: 0.8166 (t80) cc_final: 0.7722 (t80) REVERT: B 290 SER cc_start: 0.8614 (t) cc_final: 0.8304 (p) REVERT: B 320 MET cc_start: 0.8762 (tpp) cc_final: 0.8301 (mmt) outliers start: 13 outliers final: 11 residues processed: 91 average time/residue: 0.1431 time to fit residues: 19.0048 Evaluate side-chains 91 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 343 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.0970 chunk 60 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6868 Z= 0.187 Angle : 0.469 5.240 9282 Z= 0.245 Chirality : 0.040 0.139 1004 Planarity : 0.004 0.033 1113 Dihedral : 16.606 179.600 1194 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 2.33 % Allowed : 11.63 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.17 (0.31), residues: 776 helix: 2.52 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -1.59 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 199 HIS 0.003 0.001 HIS A 164 PHE 0.012 0.001 PHE A 275 TYR 0.012 0.001 TYR B 156 ARG 0.007 0.000 ARG B 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 290 SER cc_start: 0.8639 (t) cc_final: 0.8344 (p) REVERT: B 69 TYR cc_start: 0.8618 (m-80) cc_final: 0.8316 (m-80) REVERT: B 99 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6437 (p0) REVERT: B 224 PHE cc_start: 0.8165 (t80) cc_final: 0.7721 (t80) REVERT: B 290 SER cc_start: 0.8610 (t) cc_final: 0.8303 (p) REVERT: B 320 MET cc_start: 0.8760 (tpp) cc_final: 0.8287 (mmt) outliers start: 14 outliers final: 13 residues processed: 91 average time/residue: 0.1496 time to fit residues: 19.9693 Evaluate side-chains 94 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 343 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.210194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.159371 restraints weight = 18086.982| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 5.62 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6868 Z= 0.219 Angle : 0.487 5.299 9282 Z= 0.254 Chirality : 0.040 0.134 1004 Planarity : 0.004 0.036 1113 Dihedral : 16.634 179.633 1194 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.32 % Rotamer: Outliers : 2.33 % Allowed : 11.77 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.09 (0.31), residues: 776 helix: 2.46 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -1.63 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 199 HIS 0.003 0.001 HIS A 164 PHE 0.013 0.001 PHE A 275 TYR 0.013 0.001 TYR B 156 ARG 0.007 0.000 ARG B 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1481.76 seconds wall clock time: 28 minutes 10.23 seconds (1690.23 seconds total)