Starting phenix.real_space_refine on Wed Feb 12 10:51:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sfj_25079/02_2025/7sfj_25079.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sfj_25079/02_2025/7sfj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sfj_25079/02_2025/7sfj_25079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sfj_25079/02_2025/7sfj_25079.map" model { file = "/net/cci-nas-00/data/ceres_data/7sfj_25079/02_2025/7sfj_25079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sfj_25079/02_2025/7sfj_25079.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7377 Number of models: 1 Model: "" Number of chains: 8 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: "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: 251 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'RET:plan-5': 1, 'PEE:plan-1': 6, 'PEE:plan-2': 4} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Unusual residues: {'PEE': 4, 'RET': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'RET:plan-5': 1, 'PEE:plan-1': 3, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 21 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: 171 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'RET:plan-5': 1, 'PEE:plan-1': 4, 'PEE:plan-2': 2} 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} Restraints were copied for chains: B Time building chain proxies: 5.74, per 1000 atoms: 0.78 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: 1.94 Conformation dependent library (CDL) restraints added in 934.3 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: 0.58 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: 1.86 Time building geometry restraints manager: 2.24 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: 4127 30.46 - 60.91: 175 60.91 - 91.37: 12 91.37 - 121.83: 9 121.83 - 152.28: 9 Dihedral angle restraints: 4332 sinusoidal: 1857 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 4329 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: 0.880 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.470 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 7584 Z= 0.491 Angle : 0.940 12.201 10179 Z= 0.400 Chirality : 0.040 0.184 1011 Planarity : 0.005 0.047 1242 Dihedral : 18.487 152.281 2766 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.87 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (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 TRP 0.009 0.001 TRP C 177 HIS 0.003 0.001 HIS B 33 PHE 0.010 0.001 PHE A 173 TYR 0.012 0.001 TYR A 271 ARG 0.003 0.000 ARG B 266 *********************** 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 : 0.819 Fit side-chains revert: symmetry clash REVERT: B 122 MET cc_start: 0.8558 (mtt) cc_final: 0.8328 (mtm) REVERT: C 117 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8300 (ttm) outliers start: 9 outliers final: 0 residues processed: 90 average time/residue: 1.4508 time to fit residues: 137.5474 Evaluate side-chains 63 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 70 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3720 r_free = 0.3720 target = 0.135608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110453 restraints weight = 8285.887| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.95 r_work: 0.3308 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7584 Z= 0.294 Angle : 0.553 5.162 10179 Z= 0.287 Chirality : 0.041 0.130 1011 Planarity : 0.004 0.049 1242 Dihedral : 16.508 127.560 1314 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.42 % Allowed : 8.26 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.29), residues: 843 helix: 2.18 (0.21), residues: 588 sheet: None (None), residues: 0 loop : 1.10 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 19 HIS 0.004 0.001 HIS C 3 PHE 0.018 0.002 PHE B 173 TYR 0.023 0.002 TYR C 271 ARG 0.003 0.001 ARG A 195 *********************** 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 77 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.790 Fit side-chains REVERT: A 68 GLN cc_start: 0.6389 (OUTLIER) cc_final: 0.6002 (mm-40) REVERT: A 260 TYR cc_start: 0.8136 (t80) cc_final: 0.7662 (t80) REVERT: A 277 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.5803 (mpt-90) REVERT: B 68 GLN cc_start: 0.6799 (OUTLIER) cc_final: 0.6452 (mt0) REVERT: C 117 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8771 (ttm) REVERT: C 277 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.5422 (mpt-90) outliers start: 10 outliers final: 2 residues processed: 69 average time/residue: 1.5923 time to fit residues: 115.1688 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 : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 277 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.134593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109585 restraints weight = 8456.195| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.04 r_work: 0.3299 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7584 Z= 0.251 Angle : 0.508 4.705 10179 Z= 0.265 Chirality : 0.040 0.127 1011 Planarity : 0.004 0.049 1242 Dihedral : 14.944 112.247 1314 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.28 % Allowed : 11.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.29), residues: 843 helix: 2.31 (0.22), residues: 588 sheet: None (None), residues: 0 loop : 0.92 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 19 HIS 0.003 0.001 HIS C 3 PHE 0.015 0.002 PHE A 173 TYR 0.023 0.002 TYR B 271 ARG 0.002 0.000 ARG A 235 *********************** 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 74 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.750 Fit side-chains REVERT: A 68 GLN cc_start: 0.6355 (OUTLIER) cc_final: 0.5997 (mm-40) REVERT: A 260 TYR cc_start: 0.8114 (t80) cc_final: 0.7665 (t80) REVERT: A 277 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.5829 (mpt-90) REVERT: C 68 GLN cc_start: 0.6653 (OUTLIER) cc_final: 0.6434 (mm-40) REVERT: C 277 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.5483 (mpt-90) outliers start: 16 outliers final: 3 residues processed: 64 average time/residue: 1.9144 time to fit residues: 127.6760 Evaluate side-chains 63 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 271 TYR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 277 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112431 restraints weight = 8409.916| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.04 r_work: 0.3338 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7584 Z= 0.171 Angle : 0.451 4.617 10179 Z= 0.235 Chirality : 0.037 0.122 1011 Planarity : 0.004 0.048 1242 Dihedral : 13.355 111.889 1311 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.28 % Allowed : 13.39 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.29), residues: 843 helix: 2.56 (0.21), residues: 585 sheet: None (None), residues: 0 loop : 0.78 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 19 HIS 0.002 0.001 HIS C 3 PHE 0.011 0.001 PHE B 173 TYR 0.012 0.001 TYR C 271 ARG 0.002 0.000 ARG A 235 *********************** 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 69 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.715 Fit side-chains REVERT: A 68 GLN cc_start: 0.6286 (mt0) cc_final: 0.5961 (mm-40) REVERT: A 269 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7225 (mttm) REVERT: B 164 ARG cc_start: 0.6860 (tmt170) cc_final: 0.6440 (tmt170) REVERT: C 68 GLN cc_start: 0.6380 (OUTLIER) cc_final: 0.6165 (mm-40) outliers start: 9 outliers final: 2 residues processed: 62 average time/residue: 1.7816 time to fit residues: 115.4588 Evaluate side-chains 63 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 138 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.133941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109130 restraints weight = 8446.635| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.03 r_work: 0.3291 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7584 Z= 0.238 Angle : 0.492 4.702 10179 Z= 0.256 Chirality : 0.039 0.125 1011 Planarity : 0.004 0.049 1242 Dihedral : 13.688 112.862 1311 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.42 % Allowed : 12.82 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.29), residues: 843 helix: 2.45 (0.21), residues: 588 sheet: None (None), residues: 0 loop : 0.76 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 19 HIS 0.002 0.001 HIS A 33 PHE 0.014 0.001 PHE C 173 TYR 0.019 0.002 TYR B 271 ARG 0.002 0.000 ARG A 235 *********************** 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 79 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.811 Fit side-chains REVERT: A 68 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.6051 (mm-40) REVERT: B 10 MET cc_start: 0.8132 (mtm) cc_final: 0.7784 (mtp) REVERT: B 164 ARG cc_start: 0.6916 (tmt170) cc_final: 0.6462 (tmt170) REVERT: C 68 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6431 (mm-40) outliers start: 17 outliers final: 3 residues processed: 72 average time/residue: 1.7421 time to fit residues: 130.9045 Evaluate side-chains 65 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 138 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 21 optimal weight: 3.9990 chunk 83 optimal weight: 0.0570 chunk 59 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN C 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.137747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.113070 restraints weight = 8410.514| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.02 r_work: 0.3348 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7584 Z= 0.146 Angle : 0.434 4.597 10179 Z= 0.226 Chirality : 0.037 0.120 1011 Planarity : 0.003 0.047 1242 Dihedral : 12.836 112.112 1311 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.57 % Allowed : 14.39 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.29), residues: 843 helix: 2.70 (0.21), residues: 585 sheet: None (None), residues: 0 loop : 0.72 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 177 HIS 0.002 0.001 HIS B 96 PHE 0.010 0.001 PHE C 173 TYR 0.010 0.001 TYR C 271 ARG 0.002 0.000 ARG A 277 *********************** 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 69 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.723 Fit side-chains REVERT: A 68 GLN cc_start: 0.6146 (OUTLIER) cc_final: 0.5804 (mm-40) REVERT: A 269 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7234 (mttm) REVERT: B 10 MET cc_start: 0.8107 (mtm) cc_final: 0.7757 (mtp) REVERT: B 152 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7039 (mm) REVERT: C 68 GLN cc_start: 0.6353 (OUTLIER) cc_final: 0.6140 (mm-40) outliers start: 11 outliers final: 6 residues processed: 63 average time/residue: 1.8779 time to fit residues: 123.7155 Evaluate side-chains 64 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 269 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 63 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 192 GLN B 192 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.134174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109579 restraints weight = 8416.356| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.01 r_work: 0.3298 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7584 Z= 0.221 Angle : 0.477 4.642 10179 Z= 0.248 Chirality : 0.039 0.123 1011 Planarity : 0.004 0.048 1242 Dihedral : 13.218 113.195 1311 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.85 % Allowed : 13.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.29), residues: 843 helix: 2.57 (0.21), residues: 588 sheet: None (None), residues: 0 loop : 0.76 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 19 HIS 0.002 0.001 HIS B 96 PHE 0.013 0.001 PHE C 173 TYR 0.017 0.001 TYR B 271 ARG 0.002 0.000 ARG C 277 *********************** 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 82 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.713 Fit side-chains REVERT: A 68 GLN cc_start: 0.6323 (OUTLIER) cc_final: 0.5966 (mm-40) REVERT: A 269 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7296 (mttm) REVERT: B 10 MET cc_start: 0.8131 (mtm) cc_final: 0.7799 (mtp) REVERT: B 152 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7164 (mm) REVERT: B 164 ARG cc_start: 0.6911 (tmt170) cc_final: 0.6415 (tmt170) REVERT: B 221 MET cc_start: 0.6202 (mtt) cc_final: 0.5493 (pp-130) REVERT: C 68 GLN cc_start: 0.6591 (OUTLIER) cc_final: 0.6373 (mm-40) outliers start: 20 outliers final: 7 residues processed: 76 average time/residue: 1.5490 time to fit residues: 123.3972 Evaluate side-chains 70 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 189 VAL 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 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 0 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 55 optimal weight: 0.0020 chunk 49 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.136211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111931 restraints weight = 8466.318| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.97 r_work: 0.3338 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7584 Z= 0.157 Angle : 0.446 4.572 10179 Z= 0.231 Chirality : 0.037 0.127 1011 Planarity : 0.004 0.047 1242 Dihedral : 12.720 112.612 1311 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.61 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.29), residues: 843 helix: 2.72 (0.21), residues: 585 sheet: None (None), residues: 0 loop : 0.68 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 19 HIS 0.002 0.001 HIS B 96 PHE 0.011 0.001 PHE C 173 TYR 0.012 0.001 TYR B 271 ARG 0.002 0.000 ARG C 277 *********************** 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 76 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.854 Fit side-chains REVERT: A 68 GLN cc_start: 0.6200 (OUTLIER) cc_final: 0.5850 (mm-40) REVERT: A 164 ARG cc_start: 0.7461 (ptt90) cc_final: 0.6744 (ptp-170) REVERT: A 269 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7301 (mttm) REVERT: B 10 MET cc_start: 0.8165 (mtm) cc_final: 0.7837 (mtp) REVERT: B 152 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7192 (mm) REVERT: B 221 MET cc_start: 0.6593 (mtt) cc_final: 0.5685 (pp-130) REVERT: C 68 GLN cc_start: 0.6383 (OUTLIER) cc_final: 0.6148 (mm-40) outliers start: 15 outliers final: 6 residues processed: 70 average time/residue: 1.7884 time to fit residues: 131.3204 Evaluate side-chains 68 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 269 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 68 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 27 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.138569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114097 restraints weight = 8425.280| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.02 r_work: 0.3365 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7584 Z= 0.133 Angle : 0.432 4.576 10179 Z= 0.222 Chirality : 0.038 0.213 1011 Planarity : 0.003 0.046 1242 Dihedral : 12.271 112.541 1311 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.14 % Allowed : 14.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.29), residues: 843 helix: 2.80 (0.21), residues: 585 sheet: None (None), residues: 0 loop : 0.65 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 19 HIS 0.002 0.000 HIS B 96 PHE 0.010 0.001 PHE C 173 TYR 0.010 0.001 TYR B 168 ARG 0.002 0.000 ARG C 277 *********************** 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 78 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.824 Fit side-chains REVERT: A 68 GLN cc_start: 0.6081 (OUTLIER) cc_final: 0.5731 (mm-40) REVERT: A 164 ARG cc_start: 0.7386 (ptt90) cc_final: 0.6669 (ptp-170) REVERT: A 269 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7192 (mttm) REVERT: B 10 MET cc_start: 0.8072 (mtm) cc_final: 0.7740 (mtp) REVERT: B 152 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7108 (mm) REVERT: B 164 ARG cc_start: 0.6745 (tmt170) cc_final: 0.6215 (tmt170) REVERT: B 221 MET cc_start: 0.6567 (mtt) cc_final: 0.5679 (pp-130) REVERT: C 68 GLN cc_start: 0.6437 (OUTLIER) cc_final: 0.6189 (mm-40) REVERT: C 221 MET cc_start: 0.6707 (mtm) cc_final: 0.5920 (pp-130) outliers start: 15 outliers final: 5 residues processed: 71 average time/residue: 1.7419 time to fit residues: 129.4677 Evaluate side-chains 69 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 189 VAL Chi-restraints excluded: chain A residue 269 LYS 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 63 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110845 restraints weight = 8558.740| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.03 r_work: 0.3316 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7584 Z= 0.186 Angle : 0.470 6.007 10179 Z= 0.242 Chirality : 0.039 0.253 1011 Planarity : 0.004 0.047 1242 Dihedral : 12.717 113.047 1311 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.71 % Allowed : 14.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.29), residues: 843 helix: 2.68 (0.21), residues: 585 sheet: None (None), residues: 0 loop : 0.69 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 19 HIS 0.002 0.001 HIS B 96 PHE 0.013 0.001 PHE C 173 TYR 0.015 0.001 TYR B 271 ARG 0.002 0.000 ARG A 277 ********************** 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 72 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.748 Fit side-chains REVERT: A 68 GLN cc_start: 0.6216 (OUTLIER) cc_final: 0.5861 (mm-40) REVERT: A 164 ARG cc_start: 0.7494 (ptt90) cc_final: 0.6759 (ptp-170) REVERT: A 269 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7354 (mttm) REVERT: B 10 MET cc_start: 0.8179 (mtm) cc_final: 0.7866 (mtp) REVERT: B 152 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7193 (mm) REVERT: B 164 ARG cc_start: 0.6828 (tmt170) cc_final: 0.6300 (tmt170) REVERT: B 221 MET cc_start: 0.6607 (mtt) cc_final: 0.5788 (pp-130) REVERT: C 68 GLN cc_start: 0.6350 (OUTLIER) cc_final: 0.6098 (mm-40) REVERT: C 221 MET cc_start: 0.6672 (mtm) cc_final: 0.5960 (pp-130) outliers start: 12 outliers final: 7 residues processed: 68 average time/residue: 1.7607 time to fit residues: 125.1858 Evaluate side-chains 71 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 189 VAL Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain B residue 147 LEU 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 147 LEU 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 5 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.132062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107883 restraints weight = 8455.678| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.95 r_work: 0.3283 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7584 Z= 0.270 Angle : 0.526 6.178 10179 Z= 0.271 Chirality : 0.042 0.253 1011 Planarity : 0.004 0.049 1242 Dihedral : 13.428 113.476 1311 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.85 % Allowed : 14.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.29), residues: 843 helix: 2.43 (0.21), residues: 588 sheet: None (None), residues: 0 loop : 0.73 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 19 HIS 0.003 0.001 HIS C 3 PHE 0.014 0.002 PHE A 173 TYR 0.022 0.002 TYR B 271 ARG 0.002 0.000 ARG A 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4664.61 seconds wall clock time: 83 minutes 16.44 seconds (4996.44 seconds total)