Starting phenix.real_space_refine on Thu Jul 2 08:08:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sfj_25079/07_2026/7sfj_25079.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sfj_25079/07_2026/7sfj_25079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7sfj_25079/07_2026/7sfj_25079.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sfj_25079/07_2026/7sfj_25079.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sfj_25079/07_2026/7sfj_25079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sfj_25079/07_2026/7sfj_25079.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sfj_25079/07_2026/7sfj_25079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sfj_25079/07_2026/7sfj_25079.map" } resolution = 2.74 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= 0.003 sd= 0.175 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 48 5.16 5 C 4983 2.51 5 N 1098 2.21 5 O 1245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7377 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2299 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2299 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2299 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 8, 'TRANS': 275} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 168 Unusual residues: {'PEE': 8, 'RET': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PEE:plan-2': 4, 'PEE:plan-1': 6, 'RET:plan-5': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 159 Unusual residues: {'PEE': 7, 'RET': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PEE:plan-2': 3, 'PEE:plan-1': 5, 'RET:plan-5': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 150 Unusual residues: {'PEE': 6, 'RET': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PEE:plan-1': 4, 'PEE:plan-2': 2, 'RET:plan-5': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.63, per 1000 atoms: 0.22 Number of scatterers: 7377 At special positions: 0 Unit cell: (78.453, 77.316, 88.686, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 3 15.00 O 1245 8.00 N 1098 7.00 C 4983 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 375.2 milliseconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 3 sheets defined 74.3% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 26 through 53 Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.597A pdb=" N TYR A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 72 through 95 removed outlier: 3.515A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.748A pdb=" N THR A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 164 through 200 removed outlier: 3.936A pdb=" N TYR A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 222 removed outlier: 3.711A pdb=" N LEU A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 244 through 268 removed outlier: 3.884A pdb=" N CYS A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 283 removed outlier: 3.739A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 26 through 53 Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.596A pdb=" N TYR B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 72 through 95 removed outlier: 3.515A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 130 removed outlier: 3.749A pdb=" N THR B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 136 through 158 Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 164 through 200 removed outlier: 3.936A pdb=" N TYR B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 222 removed outlier: 3.710A pdb=" N LEU B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 244 through 268 removed outlier: 3.884A pdb=" N CYS B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 283 removed outlier: 3.739A pdb=" N GLY B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 53 Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.596A pdb=" N TYR C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 72 through 95 removed outlier: 3.515A pdb=" N GLY C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 130 removed outlier: 3.748A pdb=" N THR C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Proline residue: C 121 - end of helix Processing helix chain 'C' and resid 136 through 158 Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 164 through 200 removed outlier: 3.935A pdb=" N TYR C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 222 removed outlier: 3.711A pdb=" N LEU C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 211 " --> pdb=" O HIS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 244 through 268 removed outlier: 3.883A pdb=" N CYS C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 283 removed outlier: 3.739A pdb=" N GLY C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 4.573A pdb=" N ALA A 4 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 7 " --> pdb=" O ALA A 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 4 removed outlier: 4.572A pdb=" N ALA B 4 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 7 " --> pdb=" O ALA B 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 4 removed outlier: 4.572A pdb=" N ALA C 4 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 7 " --> pdb=" O ALA C 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 444 hydrogen bonds defined for protein. 1305 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: 1.02 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2079 1.34 - 1.46: 1569 1.46 - 1.57: 3858 1.57 - 1.69: 3 1.69 - 1.81: 75 Bond restraints: 7584 Sorted by residual: bond pdb=" C30 PEE B 403 " pdb=" O5 PEE B 403 " ideal model delta sigma weight residual 1.206 1.353 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C30 PEE A 403 " pdb=" O5 PEE A 403 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" C10 PEE A 401 " pdb=" O4 PEE A 401 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" C10 PEE C 403 " pdb=" O4 PEE C 403 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" C30 PEE C 405 " pdb=" O5 PEE C 405 " ideal model delta sigma weight residual 1.206 1.352 -0.146 2.00e-02 2.50e+03 5.32e+01 ... (remaining 7579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 9797 2.44 - 4.88: 346 4.88 - 7.32: 18 7.32 - 9.76: 12 9.76 - 12.20: 6 Bond angle restraints: 10179 Sorted by residual: angle pdb=" C11 PEE C 403 " pdb=" C10 PEE C 403 " pdb=" O2 PEE C 403 " ideal model delta sigma weight residual 111.70 123.90 -12.20 3.00e+00 1.11e-01 1.65e+01 angle pdb=" C11 PEE B 401 " pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 111.70 123.87 -12.17 3.00e+00 1.11e-01 1.65e+01 angle pdb=" C11 PEE A 401 " pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " ideal model delta sigma weight residual 111.70 123.86 -12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" C31 PEE B 403 " pdb=" C30 PEE B 403 " pdb=" O3 PEE B 403 " ideal model delta sigma weight residual 111.87 123.93 -12.06 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C31 PEE A 403 " pdb=" C30 PEE A 403 " pdb=" O3 PEE A 403 " ideal model delta sigma weight residual 111.87 123.88 -12.01 3.00e+00 1.11e-01 1.60e+01 ... (remaining 10174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.46: 4106 30.46 - 60.91: 166 60.91 - 91.37: 12 91.37 - 121.83: 9 121.83 - 152.28: 9 Dihedral angle restraints: 4302 sinusoidal: 1827 harmonic: 2475 Sorted by residual: dihedral pdb=" C32 PEE B 406 " pdb=" C30 PEE B 406 " pdb=" C31 PEE B 406 " pdb=" O3 PEE B 406 " ideal model delta sinusoidal sigma weight residual 161.16 8.88 152.28 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C32 PEE A 407 " pdb=" C30 PEE A 407 " pdb=" C31 PEE A 407 " pdb=" O3 PEE A 407 " ideal model delta sinusoidal sigma weight residual 161.16 8.88 152.28 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C32 PEE C 401 " pdb=" C30 PEE C 401 " pdb=" C31 PEE C 401 " pdb=" O3 PEE C 401 " ideal model delta sinusoidal sigma weight residual 161.16 8.93 152.23 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 4299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 707 0.037 - 0.074: 237 0.074 - 0.111: 52 0.111 - 0.147: 12 0.147 - 0.184: 3 Chirality restraints: 1011 Sorted by residual: chirality pdb=" CB ILE B 224 " pdb=" CA ILE B 224 " pdb=" CG1 ILE B 224 " pdb=" CG2 ILE B 224 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CB ILE A 224 " pdb=" CA ILE A 224 " pdb=" CG1 ILE A 224 " pdb=" CG2 ILE A 224 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CB ILE C 224 " pdb=" CA ILE C 224 " pdb=" CG1 ILE C 224 " pdb=" CG2 ILE C 224 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 1008 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 233 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 234 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 233 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO C 234 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 234 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 234 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 233 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO B 234 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " 0.026 5.00e-02 4.00e+02 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2269 2.83 - 3.34: 6885 3.34 - 3.86: 12038 3.86 - 4.38: 14221 4.38 - 4.90: 24644 Nonbonded interactions: 60057 Sorted by model distance: nonbonded pdb=" NH1 ARG A 195 " pdb=" O LEU A 282 " model vdw 2.308 3.120 nonbonded pdb=" NH1 ARG C 195 " pdb=" O LEU C 282 " model vdw 2.308 3.120 nonbonded pdb=" NH1 ARG B 195 " pdb=" O LEU B 282 " model vdw 2.308 3.120 nonbonded pdb=" OG SER B 51 " pdb=" OD1 ASN B 72 " model vdw 2.314 3.040 nonbonded pdb=" OG SER A 51 " pdb=" OD1 ASN A 72 " model vdw 2.314 3.040 ... (remaining 60052 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 2 through 285 or (resid 402 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42)) or (resid 404 and (nam \ e C39 or name C40 or name C41 or name C42)))) selection = (chain 'B' and (resid 2 through 285 or (resid 402 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42)) or (resid 404 and (nam \ e C39 or name C40 or name C41 or name C42)))) selection = (chain 'C' and (resid 2 through 285 or (resid 402 and (name C36 or name C37 or n \ ame C38 or name C39 or name C40 or name C41 or name C42)) or (resid 404 and (nam \ e C39 or name C40 or name C41 or name C42)))) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.850 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 0.007 0.147 7587 Z= 0.345 Angle : 0.940 12.201 10179 Z= 0.400 Chirality : 0.040 0.184 1011 Planarity : 0.005 0.047 1242 Dihedral : 18.409 152.281 2736 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.28 % Allowed : 1.28 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.20 (0.28), residues: 843 helix: 1.78 (0.21), residues: 579 sheet: None (None), residues: 0 loop : 0.95 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 266 TYR 0.012 0.001 TYR A 271 PHE 0.010 0.001 PHE A 173 TRP 0.009 0.001 TRP C 177 HIS 0.003 0.001 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.35 ( 7584) covalent geometry : angle 0.94045 / 0.40 (10179) hydrogen bonds : bond 0.12550 / 8.71 ( 444) hydrogen bonds : angle 5.18080 / 3.70 ( 1305) Misc. bond : bond 0.00027 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: B 117 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8402 (ttp) REVERT: B 122 MET cc_start: 0.8558 (mtt) cc_final: 0.8329 (mtm) REVERT: C 117 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8299 (ttm) outliers start: 9 outliers final: 0 residues processed: 90 average time/residue: 0.6250 time to fit residues: 59.0141 Evaluate side-chains 64 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain C residue 117 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 3 HIS C 192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.137849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112133 restraints weight = 8389.187| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.06 r_work: 0.3328 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7587 Z= 0.155 Angle : 0.514 5.014 10179 Z= 0.268 Chirality : 0.039 0.124 1011 Planarity : 0.004 0.047 1242 Dihedral : 15.823 120.430 1287 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.42 % Allowed : 7.98 % Favored : 90.60 % 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: 2.90 (0.29), residues: 843 helix: 2.35 (0.21), residues: 585 sheet: None (None), residues: 0 loop : 1.08 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 195 TYR 0.018 0.002 TYR C 271 PHE 0.017 0.002 PHE B 173 TRP 0.022 0.002 TRP C 19 HIS 0.003 0.001 HIS C 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 7584) covalent geometry : angle 0.51404 / 0.27 (10179) hydrogen bonds : bond 0.05569 / 3.74 ( 444) hydrogen bonds : angle 3.41408 / 2.46 ( 1305) Misc. bond : bond 0.00011 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.251 Fit side-chains REVERT: A 68 GLN cc_start: 0.6331 (OUTLIER) cc_final: 0.5955 (mm-40) REVERT: A 260 TYR cc_start: 0.8065 (t80) cc_final: 0.7481 (t80) REVERT: B 24 LYS cc_start: 0.6969 (mttt) cc_final: 0.6747 (mttp) REVERT: B 68 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.6271 (mt0) REVERT: C 68 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.6295 (mm-40) REVERT: C 117 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8748 (ttm) outliers start: 10 outliers final: 1 residues processed: 65 average time/residue: 0.6664 time to fit residues: 45.3326 Evaluate side-chains 62 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 117 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN B 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113283 restraints weight = 8363.548| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.04 r_work: 0.3346 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7587 Z= 0.122 Angle : 0.455 4.844 10179 Z= 0.237 Chirality : 0.038 0.124 1011 Planarity : 0.004 0.047 1242 Dihedral : 13.675 110.938 1284 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.99 % Allowed : 10.97 % Favored : 87.04 % 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: 3.18 (0.29), residues: 843 helix: 2.61 (0.22), residues: 585 sheet: None (None), residues: 0 loop : 1.04 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 277 TYR 0.014 0.001 TYR C 271 PHE 0.012 0.001 PHE B 173 TRP 0.015 0.001 TRP C 19 HIS 0.002 0.001 HIS C 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 7584) covalent geometry : angle 0.45455 / 0.24 (10179) hydrogen bonds : bond 0.04884 / 3.28 ( 444) hydrogen bonds : angle 3.22858 / 2.32 ( 1305) Misc. bond : bond 0.00012 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.248 Fit side-chains REVERT: A 68 GLN cc_start: 0.6277 (OUTLIER) cc_final: 0.5967 (mm-40) REVERT: A 269 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7236 (mttm) REVERT: B 10 MET cc_start: 0.8124 (mtm) cc_final: 0.7776 (mtp) REVERT: C 117 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8736 (ttm) outliers start: 14 outliers final: 1 residues processed: 61 average time/residue: 0.7926 time to fit residues: 50.4085 Evaluate side-chains 60 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain C residue 117 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113009 restraints weight = 8478.111| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.04 r_work: 0.3339 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7587 Z= 0.119 Angle : 0.447 4.631 10179 Z= 0.234 Chirality : 0.037 0.123 1011 Planarity : 0.004 0.046 1242 Dihedral : 12.944 111.279 1284 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.28 % Allowed : 12.54 % Favored : 86.18 % 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: 3.17 (0.29), residues: 843 helix: 2.67 (0.21), residues: 585 sheet: None (None), residues: 0 loop : 0.85 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 277 TYR 0.013 0.001 TYR C 271 PHE 0.012 0.001 PHE B 173 TRP 0.014 0.001 TRP C 19 HIS 0.002 0.001 HIS C 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 7584) covalent geometry : angle 0.44682 / 0.23 (10179) hydrogen bonds : bond 0.04803 / 3.22 ( 444) hydrogen bonds : angle 3.16563 / 2.27 ( 1305) Misc. bond : bond 0.00014 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.247 Fit side-chains REVERT: A 68 GLN cc_start: 0.6329 (OUTLIER) cc_final: 0.6019 (mm-40) REVERT: A 269 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7271 (mttm) REVERT: B 68 GLN cc_start: 0.6807 (mm-40) cc_final: 0.6602 (mm-40) REVERT: B 117 MET cc_start: 0.8959 (ttp) cc_final: 0.8697 (ttp) REVERT: B 269 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7238 (mttm) REVERT: C 68 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.6184 (mm-40) REVERT: C 221 MET cc_start: 0.6875 (mtt) cc_final: 0.6673 (mtt) outliers start: 9 outliers final: 3 residues processed: 63 average time/residue: 0.6962 time to fit residues: 45.7601 Evaluate side-chains 66 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 68 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.139589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114485 restraints weight = 8360.969| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.05 r_work: 0.3362 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7587 Z= 0.103 Angle : 0.424 4.647 10179 Z= 0.221 Chirality : 0.036 0.121 1011 Planarity : 0.003 0.045 1242 Dihedral : 12.423 111.230 1281 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.28 % Allowed : 13.11 % Favored : 85.61 % 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: 3.29 (0.29), residues: 843 helix: 2.76 (0.21), residues: 588 sheet: None (None), residues: 0 loop : 0.87 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 277 TYR 0.011 0.001 TYR C 271 PHE 0.011 0.001 PHE B 173 TRP 0.012 0.001 TRP C 19 HIS 0.002 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 7584) covalent geometry : angle 0.42384 / 0.22 (10179) hydrogen bonds : bond 0.04403 / 2.95 ( 444) hydrogen bonds : angle 3.09081 / 2.22 ( 1305) Misc. bond : bond 0.00017 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.243 Fit side-chains REVERT: A 68 GLN cc_start: 0.6102 (mt0) cc_final: 0.5727 (mm-40) REVERT: A 269 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7230 (mttm) REVERT: B 10 MET cc_start: 0.8010 (mtm) cc_final: 0.7659 (mtp) REVERT: B 269 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7169 (mttm) REVERT: C 68 GLN cc_start: 0.6555 (OUTLIER) cc_final: 0.6310 (mm-40) outliers start: 9 outliers final: 3 residues processed: 64 average time/residue: 0.7240 time to fit residues: 48.3847 Evaluate side-chains 64 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 68 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN B 192 GLN C 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108081 restraints weight = 8478.049| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.02 r_work: 0.3276 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7587 Z= 0.190 Angle : 0.519 4.774 10179 Z= 0.271 Chirality : 0.040 0.127 1011 Planarity : 0.004 0.049 1242 Dihedral : 13.716 112.980 1281 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.85 % Allowed : 12.68 % Favored : 84.47 % 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: 2.92 (0.29), residues: 843 helix: 2.42 (0.21), residues: 591 sheet: None (None), residues: 0 loop : 0.87 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 277 TYR 0.024 0.002 TYR C 271 PHE 0.016 0.002 PHE B 173 TRP 0.020 0.002 TRP C 19 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 ( 7584) covalent geometry : angle 0.51909 / 0.27 (10179) hydrogen bonds : bond 0.05861 / 3.90 ( 444) hydrogen bonds : angle 3.31560 / 2.38 ( 1305) Misc. bond : bond 0.00007 / 0.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.227 Fit side-chains REVERT: A 68 GLN cc_start: 0.6255 (OUTLIER) cc_final: 0.5927 (mm-40) REVERT: B 10 MET cc_start: 0.8184 (mtm) cc_final: 0.7845 (mtp) REVERT: B 221 MET cc_start: 0.6319 (mtm) cc_final: 0.5524 (pp-130) REVERT: B 269 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7297 (mttm) REVERT: C 68 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.6378 (mm-40) REVERT: C 260 TYR cc_start: 0.8052 (t80) cc_final: 0.7708 (t80) outliers start: 20 outliers final: 4 residues processed: 77 average time/residue: 0.6659 time to fit residues: 53.4611 Evaluate side-chains 69 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 186 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 50 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.134487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109938 restraints weight = 8548.920| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.02 r_work: 0.3302 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7587 Z= 0.142 Angle : 0.472 4.672 10179 Z= 0.246 Chirality : 0.038 0.123 1011 Planarity : 0.004 0.049 1242 Dihedral : 13.166 112.481 1281 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.42 % Allowed : 13.39 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.95 (0.29), residues: 843 helix: 2.50 (0.21), residues: 588 sheet: None (None), residues: 0 loop : 0.74 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 277 TYR 0.015 0.001 TYR C 271 PHE 0.013 0.001 PHE B 173 TRP 0.017 0.001 TRP C 19 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 7584) covalent geometry : angle 0.47195 / 0.25 (10179) hydrogen bonds : bond 0.05101 / 3.41 ( 444) hydrogen bonds : angle 3.23306 / 2.32 ( 1305) Misc. bond : bond 0.00010 / 0.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.252 Fit side-chains REVERT: A 68 GLN cc_start: 0.6256 (OUTLIER) cc_final: 0.5860 (mm-40) REVERT: A 269 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7267 (mttm) REVERT: B 10 MET cc_start: 0.8167 (mtm) cc_final: 0.7844 (mtp) REVERT: B 117 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8659 (ttp) REVERT: B 221 MET cc_start: 0.6542 (mtm) cc_final: 0.5643 (pp-130) REVERT: C 68 GLN cc_start: 0.6531 (OUTLIER) cc_final: 0.6282 (mm-40) outliers start: 17 outliers final: 8 residues processed: 69 average time/residue: 0.6916 time to fit residues: 49.8294 Evaluate side-chains 70 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 271 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN B 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.133188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109008 restraints weight = 8570.764| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.97 r_work: 0.3291 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7587 Z= 0.161 Angle : 0.496 4.708 10179 Z= 0.258 Chirality : 0.039 0.147 1011 Planarity : 0.004 0.050 1242 Dihedral : 13.513 113.256 1281 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.56 % Allowed : 13.96 % Favored : 83.48 % 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: 2.85 (0.29), residues: 843 helix: 2.43 (0.21), residues: 588 sheet: None (None), residues: 0 loop : 0.69 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 277 TYR 0.018 0.002 TYR A 271 PHE 0.014 0.001 PHE A 173 TRP 0.019 0.001 TRP C 19 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 7584) covalent geometry : angle 0.49565 / 0.26 (10179) hydrogen bonds : bond 0.05461 / 3.65 ( 444) hydrogen bonds : angle 3.29111 / 2.36 ( 1305) Misc. bond : bond 0.00004 / 0.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.246 Fit side-chains REVERT: A 68 GLN cc_start: 0.6306 (OUTLIER) cc_final: 0.5980 (mm-40) REVERT: A 269 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7377 (mttm) REVERT: B 10 MET cc_start: 0.8202 (mtm) cc_final: 0.7881 (mtp) REVERT: B 152 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7223 (mm) REVERT: B 221 MET cc_start: 0.6593 (mtm) cc_final: 0.5797 (pp-130) REVERT: C 68 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.6369 (mm-40) outliers start: 18 outliers final: 8 residues processed: 69 average time/residue: 0.7164 time to fit residues: 51.5798 Evaluate side-chains 71 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 271 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 41 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN B 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.136214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112151 restraints weight = 8378.956| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.96 r_work: 0.3335 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7587 Z= 0.113 Angle : 0.455 5.015 10179 Z= 0.235 Chirality : 0.038 0.209 1011 Planarity : 0.004 0.048 1242 Dihedral : 12.913 112.691 1281 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.14 % Allowed : 14.53 % Favored : 83.33 % 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: 3.05 (0.29), residues: 843 helix: 2.58 (0.21), residues: 588 sheet: None (None), residues: 0 loop : 0.77 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 277 TYR 0.011 0.001 TYR C 271 PHE 0.011 0.001 PHE C 173 TRP 0.014 0.001 TRP C 19 HIS 0.002 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 7584) covalent geometry : angle 0.45458 / 0.23 (10179) hydrogen bonds : bond 0.04653 / 3.12 ( 444) hydrogen bonds : angle 3.20216 / 2.30 ( 1305) Misc. bond : bond 0.00016 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.158 Fit side-chains REVERT: A 68 GLN cc_start: 0.6203 (OUTLIER) cc_final: 0.5845 (mm-40) REVERT: A 269 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7287 (mttm) REVERT: B 10 MET cc_start: 0.8177 (mtm) cc_final: 0.7859 (mtp) REVERT: B 152 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7171 (mm) REVERT: B 221 MET cc_start: 0.6540 (mtm) cc_final: 0.5782 (pp-130) REVERT: C 68 GLN cc_start: 0.6324 (OUTLIER) cc_final: 0.6087 (mm-40) outliers start: 15 outliers final: 4 residues processed: 70 average time/residue: 0.6255 time to fit residues: 45.7085 Evaluate side-chains 67 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 18 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN B 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.133816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109784 restraints weight = 8429.559| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.95 r_work: 0.3304 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7587 Z= 0.146 Angle : 0.496 6.234 10179 Z= 0.256 Chirality : 0.040 0.250 1011 Planarity : 0.004 0.049 1242 Dihedral : 13.234 113.225 1281 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.57 % Allowed : 14.96 % Favored : 83.48 % 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: 2.92 (0.29), residues: 843 helix: 2.49 (0.21), residues: 588 sheet: None (None), residues: 0 loop : 0.70 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 277 TYR 0.016 0.001 TYR A 271 PHE 0.014 0.001 PHE C 173 TRP 0.019 0.001 TRP C 19 HIS 0.002 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 7584) covalent geometry : angle 0.49647 / 0.26 (10179) hydrogen bonds : bond 0.05184 / 3.46 ( 444) hydrogen bonds : angle 3.27576 / 2.35 ( 1305) Misc. bond : bond 0.00008 / 0.00 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.282 Fit side-chains REVERT: A 68 GLN cc_start: 0.6300 (OUTLIER) cc_final: 0.5906 (mm-40) REVERT: A 269 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7333 (mttm) REVERT: B 10 MET cc_start: 0.8189 (mtm) cc_final: 0.7875 (mtp) REVERT: B 152 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7244 (mm) REVERT: B 221 MET cc_start: 0.6544 (mtm) cc_final: 0.5755 (pp-130) REVERT: C 68 GLN cc_start: 0.6574 (OUTLIER) cc_final: 0.6321 (mm-40) outliers start: 11 outliers final: 6 residues processed: 68 average time/residue: 0.7335 time to fit residues: 52.0297 Evaluate side-chains 70 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 45 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 72 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.132202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.108158 restraints weight = 8476.048| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.95 r_work: 0.3288 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7587 Z= 0.168 Angle : 0.523 6.178 10179 Z= 0.269 Chirality : 0.041 0.247 1011 Planarity : 0.004 0.050 1242 Dihedral : 13.524 113.335 1281 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.85 % Allowed : 14.53 % Favored : 83.62 % 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: 2.80 (0.29), residues: 843 helix: 2.40 (0.21), residues: 588 sheet: None (None), residues: 0 loop : 0.67 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 277 TYR 0.019 0.002 TYR C 271 PHE 0.014 0.002 PHE B 173 TRP 0.021 0.002 TRP C 19 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 7584) covalent geometry : angle 0.52261 / 0.27 (10179) hydrogen bonds : bond 0.05515 / 3.67 ( 444) hydrogen bonds : angle 3.34353 / 2.40 ( 1305) Misc. bond : bond 0.00003 / 0.00 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2047.89 seconds wall clock time: 35 minutes 42.21 seconds (2142.21 seconds total)