Starting phenix.real_space_refine on Thu Jul 2 04:55:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8urp_42496/07_2026/8urp_42496.cif Found real_map, /net/cci-nas-00/data/ceres_data/8urp_42496/07_2026/8urp_42496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8urp_42496/07_2026/8urp_42496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8urp_42496/07_2026/8urp_42496.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8urp_42496/07_2026/8urp_42496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8urp_42496/07_2026/8urp_42496.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.067 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 12 5.49 5 Mg 4 5.21 5 S 42 5.16 5 C 4544 2.51 5 N 968 2.21 5 O 1177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6747 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" 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: "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: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 297 Unusual residues: {' MG': 2, 'CDC': 1, 'PCF': 1, 'PCW': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 187 Unusual residues: {' MG': 2, 'CDC': 1, 'PCF': 1, 'PCW': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 2.20, per 1000 atoms: 0.33 Number of scatterers: 6747 At special positions: 0 Unit cell: (75.6, 74.52, 104.76, 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 12 15.00 Mg 4 11.99 O 1177 8.00 N 968 7.00 C 4544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 406.5 milliseconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 3 sheets defined 79.6% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 removed outlier: 3.527A pdb=" N LEU A 10 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY A 11 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASN A 12 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.635A pdb=" N ASN A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 40 removed outlier: 3.877A pdb=" N THR A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 70 removed outlier: 3.524A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 106 removed outlier: 3.765A pdb=" N PHE A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 128 removed outlier: 4.184A pdb=" N THR A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 137 removed outlier: 4.054A pdb=" N VAL A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 166 removed outlier: 3.582A pdb=" N ILE A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.696A 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 216 through 248 removed outlier: 3.531A pdb=" N LEU A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 268 through 285 removed outlier: 3.523A pdb=" N PHE A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 289 Processing helix chain 'A' and resid 290 through 315 Processing helix chain 'A' and resid 322 through 325 Processing helix chain 'A' and resid 326 through 341 Processing helix chain 'A' and resid 348 through 381 removed outlier: 3.527A pdb=" N TRP A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 15 removed outlier: 4.181A pdb=" N GLY B 11 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN B 12 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 13 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 14 " --> pdb=" O GLY B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 30 through 39 removed outlier: 4.493A pdb=" N PHE B 34 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 70 removed outlier: 3.805A pdb=" N VAL B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 53 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 107 removed outlier: 3.782A pdb=" N PHE B 83 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 128 removed outlier: 3.579A pdb=" N ILE B 123 " --> pdb=" O CYS B 119 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 137 removed outlier: 4.007A pdb=" N VAL B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 166 removed outlier: 3.688A pdb=" N ILE B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 194 Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 217 through 252 removed outlier: 3.914A pdb=" N THR B 249 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 removed outlier: 3.912A pdb=" N THR B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 285 removed outlier: 3.528A pdb=" N PHE B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 315 Processing helix chain 'B' and resid 322 through 325 Processing helix chain 'B' and resid 326 through 341 Processing helix chain 'B' and resid 345 through 381 removed outlier: 3.546A pdb=" N TRP B 355 " --> pdb=" O SER B 351 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 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 207 removed outlier: 3.933A pdb=" N ALA B 204 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE B 213 " --> pdb=" O PHE B 206 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1291 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: 0.91 Time building geometry restraints manager: 0.58 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: 942 1.31 - 1.43: 2066 1.43 - 1.56: 3822 1.56 - 1.68: 31 1.68 - 1.81: 71 Bond restraints: 6932 Sorted by residual: bond pdb=" C2' CDC B 405 " pdb=" C3' CDC B 405 " ideal model delta sigma weight residual 1.533 1.291 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C2' CDC A1005 " pdb=" C3' CDC A1005 " ideal model delta sigma weight residual 1.533 1.292 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C5 CDC B 405 " pdb=" C6 CDC B 405 " ideal model delta sigma weight residual 1.346 1.489 -0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" C2 CDC B 405 " pdb=" N3 CDC B 405 " ideal model delta sigma weight residual 1.349 1.492 -0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" C2 CDC A1005 " pdb=" N3 CDC A1005 " ideal model delta sigma weight residual 1.349 1.492 -0.143 2.00e-02 2.50e+03 5.10e+01 ... (remaining 6927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 9280 5.02 - 10.04: 68 10.04 - 15.06: 21 15.06 - 20.07: 7 20.07 - 25.09: 6 Bond angle restraints: 9382 Sorted by residual: angle pdb=" C19 PCW B 401 " pdb=" C20 PCW B 401 " pdb=" C21 PCW B 401 " ideal model delta sigma weight residual 127.82 152.91 -25.09 3.00e+00 1.11e-01 7.00e+01 angle pdb=" C19 PCW A1004 " pdb=" C20 PCW A1004 " pdb=" C21 PCW A1004 " ideal model delta sigma weight residual 127.82 152.89 -25.07 3.00e+00 1.11e-01 6.99e+01 angle pdb=" C19 PCW A1007 " pdb=" C20 PCW A1007 " pdb=" C21 PCW A1007 " ideal model delta sigma weight residual 127.82 152.67 -24.85 3.00e+00 1.11e-01 6.86e+01 angle pdb=" C19 PCW A1003 " pdb=" C20 PCW A1003 " pdb=" C21 PCW A1003 " ideal model delta sigma weight residual 127.82 152.47 -24.65 3.00e+00 1.11e-01 6.75e+01 angle pdb=" C19 PCW B 404 " pdb=" C20 PCW B 404 " pdb=" C21 PCW B 404 " ideal model delta sigma weight residual 127.82 152.36 -24.54 3.00e+00 1.11e-01 6.69e+01 ... (remaining 9377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 3885 35.87 - 71.73: 199 71.73 - 107.60: 20 107.60 - 143.47: 2 143.47 - 179.33: 6 Dihedral angle restraints: 4112 sinusoidal: 1826 harmonic: 2286 Sorted by residual: 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 -0.67 -179.33 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" O21 PCF B 406 " pdb=" C2 PCF B 406 " pdb=" C3 PCF B 406 " pdb=" O31 PCF B 406 " ideal model delta sinusoidal sigma weight residual 59.47 -124.09 -176.44 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N PCW B 404 " pdb=" C4 PCW B 404 " pdb=" C5 PCW B 404 " pdb=" O4P PCW B 404 " ideal model delta sinusoidal sigma weight residual 293.34 136.86 156.48 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 4109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 859 0.058 - 0.116: 135 0.116 - 0.173: 7 0.173 - 0.231: 6 0.231 - 0.289: 3 Chirality restraints: 1010 Sorted by residual: chirality pdb=" C3' CDC B 405 " pdb=" C2' CDC B 405 " pdb=" C4' CDC B 405 " pdb=" O3' CDC B 405 " both_signs ideal model delta sigma weight residual False -2.71 -2.42 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C3' CDC A1005 " pdb=" C2' CDC A1005 " pdb=" C4' CDC A1005 " pdb=" O3' CDC A1005 " both_signs ideal model delta sigma weight residual False -2.71 -2.42 -0.29 2.00e-01 2.50e+01 2.07e+00 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 ... (remaining 1007 not shown) Planarity restraints: 1110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 175 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO A 176 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 175 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO B 176 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 176 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 176 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 285 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO B 286 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 286 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 286 " 0.016 5.00e-02 4.00e+02 ... (remaining 1107 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 58 2.58 - 3.16: 5376 3.16 - 3.74: 10217 3.74 - 4.32: 14754 4.32 - 4.90: 25058 Nonbonded interactions: 55463 Sorted by model distance: nonbonded pdb=" OD2 ASP A 121 " pdb="MG MG A1002 " model vdw 2.000 2.170 nonbonded pdb=" OD2 ASP B 121 " pdb="MG MG B 403 " model vdw 2.035 2.170 nonbonded pdb=" OD2 ASP A 117 " pdb="MG MG A1001 " model vdw 2.060 2.170 nonbonded pdb="MG MG B 402 " pdb=" O1A CDC B 405 " model vdw 2.061 2.170 nonbonded pdb="MG MG A1001 " pdb=" O2A CDC A1005 " model vdw 2.076 2.170 ... (remaining 55458 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 117 or resid 119 through 388 or resid 1002 or (r \ esid 1004 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name \ C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or n \ ame C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 o \ r name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or name C4 \ 2 or name C43 or name C44 or name C45 or name C46 or name C47 or name C48 or nam \ e C5 or name C6 or name C7 or name C8 or name O11 or name O1P or name O2 or name \ O2P or name O3 or name O31 or name O3P or name O4P or name P )) or resid 1005 t \ hrough 1006)) selection = (chain 'B' and (resid 1 through 117 or resid 119 through 388 or resid 402 or res \ id 404 through 406)) } 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=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.400 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.370 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 : 0.011 0.242 6932 Z= 0.561 Angle : 1.367 25.093 9382 Z= 0.493 Chirality : 0.046 0.289 1010 Planarity : 0.004 0.060 1110 Dihedral : 20.297 179.333 2648 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.60 % Allowed : 3.50 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.31), residues: 772 helix: 2.96 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.42 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 23 TYR 0.012 0.001 TYR B 274 PHE 0.012 0.001 PHE A 275 TRP 0.012 0.001 TRP B 160 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.01128 / 0.56 ( 6932) covalent geometry : angle 1.36725 / 0.49 ( 9382) hydrogen bonds : bond 0.11968 / 7.32 ( 439) hydrogen bonds : angle 4.73927 / 3.49 ( 1291) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 116 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7029 (t80) REVERT: B 75 GLN cc_start: 0.6709 (mt0) cc_final: 0.6147 (mt0) REVERT: B 116 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.6818 (t80) REVERT: B 162 GLU cc_start: 0.8484 (tt0) cc_final: 0.8244 (tt0) outliers start: 11 outliers final: 6 residues processed: 97 average time/residue: 0.0710 time to fit residues: 9.2140 Evaluate side-chains 89 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN B 28 ASN B 118 HIS B Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.116992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.086681 restraints weight = 91912.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.089556 restraints weight = 53725.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.086878 restraints weight = 50753.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.087272 restraints weight = 47360.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.087322 restraints weight = 46453.973| |-----------------------------------------------------------------------------| r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6932 Z= 0.112 Angle : 0.490 5.398 9382 Z= 0.250 Chirality : 0.040 0.195 1010 Planarity : 0.004 0.062 1110 Dihedral : 23.749 179.336 1293 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.75 % Allowed : 5.54 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.31), residues: 772 helix: 3.04 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.55 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 23 TYR 0.011 0.001 TYR B 274 PHE 0.014 0.001 PHE A 275 TRP 0.011 0.001 TRP B 160 HIS 0.003 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 6932) covalent geometry : angle 0.49034 / 0.25 ( 9382) hydrogen bonds : bond 0.04359 / 2.79 ( 439) hydrogen bonds : angle 4.01695 / 2.96 ( 1291) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 116 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7553 (t80) REVERT: B 28 ASN cc_start: 0.7624 (m110) cc_final: 0.7050 (m-40) REVERT: B 75 GLN cc_start: 0.6620 (mt0) cc_final: 0.6264 (mt0) REVERT: B 116 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7345 (t80) REVERT: B 162 GLU cc_start: 0.8509 (tt0) cc_final: 0.8228 (tt0) outliers start: 12 outliers final: 6 residues processed: 90 average time/residue: 0.0703 time to fit residues: 8.5147 Evaluate side-chains 87 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN A 345 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.114412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.084802 restraints weight = 97159.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.088049 restraints weight = 55243.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.085036 restraints weight = 57443.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.085473 restraints weight = 48729.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.085410 restraints weight = 48644.977| |-----------------------------------------------------------------------------| r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6932 Z= 0.142 Angle : 0.517 5.384 9382 Z= 0.263 Chirality : 0.041 0.136 1010 Planarity : 0.005 0.063 1110 Dihedral : 22.494 179.624 1291 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.60 % Allowed : 6.85 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.31), residues: 772 helix: 2.84 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.61 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 23 TYR 0.012 0.001 TYR B 274 PHE 0.015 0.001 PHE A 275 TRP 0.010 0.001 TRP B 160 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 6932) covalent geometry : angle 0.51659 / 0.26 ( 9382) hydrogen bonds : bond 0.04872 / 3.11 ( 439) hydrogen bonds : angle 3.99747 / 2.93 ( 1291) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 116 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7717 (t80) REVERT: B 28 ASN cc_start: 0.7620 (m110) cc_final: 0.6980 (m-40) REVERT: B 75 GLN cc_start: 0.6752 (mt0) cc_final: 0.6439 (mt0) REVERT: B 116 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7372 (t80) REVERT: B 162 GLU cc_start: 0.8526 (tt0) cc_final: 0.8247 (tt0) REVERT: B 345 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.6897 (mp10) outliers start: 11 outliers final: 7 residues processed: 85 average time/residue: 0.0748 time to fit residues: 8.3979 Evaluate side-chains 84 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 345 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN B 260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.115014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.085213 restraints weight = 90348.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.087994 restraints weight = 52854.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.085593 restraints weight = 47847.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.086151 restraints weight = 48288.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.085834 restraints weight = 49709.543| |-----------------------------------------------------------------------------| r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6932 Z= 0.135 Angle : 0.504 5.332 9382 Z= 0.256 Chirality : 0.041 0.135 1010 Planarity : 0.005 0.062 1110 Dihedral : 21.167 179.484 1291 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.90 % Allowed : 6.56 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.31), residues: 772 helix: 2.84 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.61 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 23 TYR 0.012 0.001 TYR B 274 PHE 0.014 0.001 PHE A 275 TRP 0.011 0.001 TRP B 160 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 ( 6932) covalent geometry : angle 0.50373 / 0.26 ( 9382) hydrogen bonds : bond 0.04655 / 2.97 ( 439) hydrogen bonds : angle 3.92804 / 2.88 ( 1291) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.205 Fit side-chains REVERT: A 116 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7642 (t80) REVERT: A 162 GLU cc_start: 0.8358 (tp30) cc_final: 0.8083 (tt0) REVERT: B 75 GLN cc_start: 0.6473 (mt0) cc_final: 0.6219 (mt0) REVERT: B 116 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7317 (t80) REVERT: B 162 GLU cc_start: 0.8430 (tt0) cc_final: 0.8173 (tt0) REVERT: B 345 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6610 (mp10) outliers start: 13 outliers final: 9 residues processed: 82 average time/residue: 0.0756 time to fit residues: 8.2811 Evaluate side-chains 84 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.0050 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 51 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN B 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.117005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.086777 restraints weight = 91097.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.089738 restraints weight = 54116.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.087549 restraints weight = 54288.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.087818 restraints weight = 48390.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.087788 restraints weight = 48182.232| |-----------------------------------------------------------------------------| r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6932 Z= 0.102 Angle : 0.458 5.215 9382 Z= 0.235 Chirality : 0.039 0.127 1010 Planarity : 0.004 0.061 1110 Dihedral : 20.100 179.252 1291 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.90 % Allowed : 6.56 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.31), residues: 772 helix: 3.06 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.59 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 242 TYR 0.011 0.001 TYR B 274 PHE 0.013 0.001 PHE A 275 TRP 0.012 0.001 TRP B 160 HIS 0.003 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 6932) covalent geometry : angle 0.45834 / 0.23 ( 9382) hydrogen bonds : bond 0.03951 / 2.52 ( 439) hydrogen bonds : angle 3.77521 / 2.77 ( 1291) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.190 Fit side-chains REVERT: A 116 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7528 (t80) REVERT: A 162 GLU cc_start: 0.8424 (tp30) cc_final: 0.8205 (tt0) REVERT: B 28 ASN cc_start: 0.7733 (m110) cc_final: 0.7427 (m-40) REVERT: B 75 GLN cc_start: 0.6532 (mt0) cc_final: 0.6290 (mt0) REVERT: B 116 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7365 (t80) REVERT: B 162 GLU cc_start: 0.8506 (tt0) cc_final: 0.8251 (tt0) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 0.0640 time to fit residues: 7.5270 Evaluate side-chains 88 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.113605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.083857 restraints weight = 86356.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.086058 restraints weight = 53699.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.084031 restraints weight = 54985.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.084346 restraints weight = 48722.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.084273 restraints weight = 49503.806| |-----------------------------------------------------------------------------| r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2513 r_free = 0.2513 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2513 r_free = 0.2513 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6932 Z= 0.158 Angle : 0.518 5.290 9382 Z= 0.265 Chirality : 0.042 0.139 1010 Planarity : 0.005 0.063 1110 Dihedral : 20.202 179.706 1291 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.48 % Allowed : 6.41 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.31), residues: 772 helix: 2.79 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.59 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 23 TYR 0.012 0.001 TYR B 274 PHE 0.016 0.001 PHE A 275 TRP 0.009 0.001 TRP B 160 HIS 0.002 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 6932) covalent geometry : angle 0.51768 / 0.27 ( 9382) hydrogen bonds : bond 0.04988 / 3.18 ( 439) hydrogen bonds : angle 3.95892 / 2.90 ( 1291) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.168 Fit side-chains REVERT: A 116 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7842 (t80) REVERT: A 162 GLU cc_start: 0.8580 (tp30) cc_final: 0.8180 (tt0) REVERT: B 28 ASN cc_start: 0.7667 (m110) cc_final: 0.7392 (m-40) REVERT: B 116 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7261 (t80) REVERT: B 162 GLU cc_start: 0.8564 (tt0) cc_final: 0.8345 (tt0) REVERT: B 345 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.6693 (mp10) outliers start: 17 outliers final: 14 residues processed: 86 average time/residue: 0.0625 time to fit residues: 7.3380 Evaluate side-chains 90 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 70 optimal weight: 0.0970 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 69 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.117117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.087539 restraints weight = 122473.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.090580 restraints weight = 61339.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.087641 restraints weight = 56261.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.088289 restraints weight = 50287.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.087921 restraints weight = 53819.273| |-----------------------------------------------------------------------------| r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6932 Z= 0.101 Angle : 0.449 5.207 9382 Z= 0.233 Chirality : 0.039 0.127 1010 Planarity : 0.004 0.060 1110 Dihedral : 19.501 179.246 1291 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.19 % Allowed : 6.85 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.31), residues: 772 helix: 3.06 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.56 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 242 TYR 0.011 0.001 TYR B 274 PHE 0.013 0.001 PHE A 275 TRP 0.011 0.001 TRP B 160 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 6932) covalent geometry : angle 0.44862 / 0.23 ( 9382) hydrogen bonds : bond 0.03943 / 2.52 ( 439) hydrogen bonds : angle 3.76388 / 2.77 ( 1291) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.149 Fit side-chains REVERT: A 116 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7561 (t80) REVERT: A 162 GLU cc_start: 0.8558 (tp30) cc_final: 0.8252 (tt0) REVERT: B 28 ASN cc_start: 0.7613 (m110) cc_final: 0.7040 (m-40) REVERT: B 116 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7274 (t80) REVERT: B 162 GLU cc_start: 0.8434 (tt0) cc_final: 0.8224 (tt0) REVERT: B 345 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6698 (mp10) outliers start: 15 outliers final: 12 residues processed: 87 average time/residue: 0.0661 time to fit residues: 7.8400 Evaluate side-chains 92 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.0570 chunk 40 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.115582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.085434 restraints weight = 130628.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.087550 restraints weight = 62381.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.085779 restraints weight = 51373.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.085954 restraints weight = 52761.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.085744 restraints weight = 52004.579| |-----------------------------------------------------------------------------| r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6932 Z= 0.121 Angle : 0.469 5.196 9382 Z= 0.243 Chirality : 0.040 0.131 1010 Planarity : 0.004 0.060 1110 Dihedral : 19.311 179.560 1291 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.19 % Allowed : 7.14 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.31), residues: 772 helix: 2.97 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.57 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 242 TYR 0.011 0.001 TYR B 274 PHE 0.014 0.001 PHE A 275 TRP 0.011 0.001 TRP B 160 HIS 0.002 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 6932) covalent geometry : angle 0.46882 / 0.24 ( 9382) hydrogen bonds : bond 0.04383 / 2.80 ( 439) hydrogen bonds : angle 3.83393 / 2.81 ( 1291) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.149 Fit side-chains REVERT: A 116 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7706 (t80) REVERT: A 162 GLU cc_start: 0.8533 (tp30) cc_final: 0.8137 (tt0) REVERT: B 28 ASN cc_start: 0.7772 (m110) cc_final: 0.7299 (m-40) REVERT: B 116 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7204 (t80) REVERT: B 162 GLU cc_start: 0.8590 (tt0) cc_final: 0.8358 (tt0) REVERT: B 345 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6754 (mp10) outliers start: 15 outliers final: 12 residues processed: 85 average time/residue: 0.0681 time to fit residues: 7.7080 Evaluate side-chains 90 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.115933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.086291 restraints weight = 133922.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.089051 restraints weight = 60239.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.086194 restraints weight = 61480.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.086460 restraints weight = 54104.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.086488 restraints weight = 53926.691| |-----------------------------------------------------------------------------| r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6932 Z= 0.114 Angle : 0.457 5.148 9382 Z= 0.238 Chirality : 0.039 0.130 1010 Planarity : 0.004 0.061 1110 Dihedral : 18.868 179.394 1291 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.48 % Allowed : 6.56 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.31), residues: 772 helix: 3.02 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.58 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 242 TYR 0.011 0.001 TYR B 274 PHE 0.014 0.001 PHE A 275 TRP 0.011 0.001 TRP B 160 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 6932) covalent geometry : angle 0.45743 / 0.24 ( 9382) hydrogen bonds : bond 0.04195 / 2.68 ( 439) hydrogen bonds : angle 3.79334 / 2.79 ( 1291) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.150 Fit side-chains REVERT: A 116 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7624 (t80) REVERT: A 162 GLU cc_start: 0.8606 (tp30) cc_final: 0.8209 (tt0) REVERT: B 28 ASN cc_start: 0.7662 (m110) cc_final: 0.7094 (m-40) REVERT: B 116 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7318 (t80) REVERT: B 162 GLU cc_start: 0.8503 (tt0) cc_final: 0.8237 (tt0) REVERT: B 345 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.6771 (mp10) outliers start: 17 outliers final: 14 residues processed: 87 average time/residue: 0.0635 time to fit residues: 7.5056 Evaluate side-chains 93 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 0.0060 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 chunk 63 optimal weight: 7.9990 chunk 45 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.119393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.089413 restraints weight = 121756.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.092208 restraints weight = 59360.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.088896 restraints weight = 69683.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.090451 restraints weight = 54040.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.089303 restraints weight = 60579.725| |-----------------------------------------------------------------------------| r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6932 Z= 0.090 Angle : 0.427 5.139 9382 Z= 0.222 Chirality : 0.038 0.123 1010 Planarity : 0.004 0.059 1110 Dihedral : 18.064 179.157 1291 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.19 % Allowed : 6.85 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.31), residues: 772 helix: 3.21 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.51 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 242 TYR 0.010 0.001 TYR B 274 PHE 0.012 0.001 PHE A 275 TRP 0.011 0.001 TRP B 160 HIS 0.003 0.000 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 ( 6932) covalent geometry : angle 0.42740 / 0.22 ( 9382) hydrogen bonds : bond 0.03519 / 2.25 ( 439) hydrogen bonds : angle 3.66353 / 2.70 ( 1291) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.214 Fit side-chains REVERT: A 116 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7505 (t80) REVERT: B 28 ASN cc_start: 0.7604 (m110) cc_final: 0.7332 (m-40) REVERT: B 116 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7312 (t80) REVERT: B 345 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6868 (mp10) outliers start: 15 outliers final: 11 residues processed: 90 average time/residue: 0.0626 time to fit residues: 7.6701 Evaluate side-chains 91 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 345 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 41 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 0.0170 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.117439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.086618 restraints weight = 125931.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.088964 restraints weight = 59278.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.087014 restraints weight = 60486.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.087505 restraints weight = 52255.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.087189 restraints weight = 57773.705| |-----------------------------------------------------------------------------| r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6932 Z= 0.121 Angle : 0.470 5.191 9382 Z= 0.245 Chirality : 0.040 0.145 1010 Planarity : 0.004 0.058 1110 Dihedral : 18.150 179.490 1291 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.19 % Allowed : 7.14 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.31), residues: 772 helix: 3.05 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.51 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 23 TYR 0.011 0.001 TYR B 274 PHE 0.014 0.001 PHE A 275 TRP 0.010 0.001 TRP B 160 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 6932) covalent geometry : angle 0.46959 / 0.25 ( 9382) hydrogen bonds : bond 0.04247 / 2.71 ( 439) hydrogen bonds : angle 3.78192 / 2.77 ( 1291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 897.01 seconds wall clock time: 16 minutes 16.21 seconds (976.21 seconds total)