Starting phenix.real_space_refine on Tue Aug 4 15:47:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xzs_72370/08_2026/9xzs_72370_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xzs_72370/08_2026/9xzs_72370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xzs_72370/08_2026/9xzs_72370_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xzs_72370/08_2026/9xzs_72370_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xzs_72370/08_2026/9xzs_72370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xzs_72370/08_2026/9xzs_72370.map" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 71 5.49 5 S 14 5.16 5 C 2578 2.51 5 N 791 2.21 5 O 1059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4513 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1513 Classifications: {'RNA': 71} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 29} Link IDs: {'rna2p': 12, 'rna3p': 58} Chain: "B" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1421 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1551 Classifications: {'peptide': 188} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 180} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'AN6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.44, per 1000 atoms: 0.32 Number of scatterers: 4513 At special positions: 0 Unit cell: (65.096, 76.632, 117.832, 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 14 16.00 P 71 15.00 O 1059 8.00 N 791 7.00 C 2578 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 124.4 milliseconds 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 690 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 3 sheets defined 38.9% alpha, 2.8% beta 19 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 108 through 127 removed outlier: 3.901A pdb=" N ILE B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 152 removed outlier: 4.033A pdb=" N ARG B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 removed outlier: 3.533A pdb=" N ASN B 159 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP B 160 " --> pdb=" O TYR B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 156 through 160' Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 216 through 225 Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'C' and resid 108 through 129 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 152 through 155 removed outlier: 3.540A pdb=" N THR C 155 " --> pdb=" O LEU C 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 155' Processing helix chain 'C' and resid 169 through 173 removed outlier: 3.504A pdb=" N MET C 172 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 247 through 262 Processing helix chain 'C' and resid 265 through 272 Processing sheet with id=AA1, first strand: chain 'B' and resid 184 through 185 removed outlier: 6.769A pdb=" N VAL B 184 " --> pdb=" O ILE B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 136 through 137 removed outlier: 4.310A pdb=" N VAL C 137 " --> pdb=" O LYS C 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 182 through 185 removed outlier: 6.607A pdb=" N LYS C 182 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE C 204 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 184 " --> pdb=" O ILE C 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 83 hydrogen bonds defined for protein. 231 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 0.60 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 610 1.31 - 1.43: 1659 1.43 - 1.56: 2309 1.56 - 1.68: 147 1.68 - 1.81: 25 Bond restraints: 4750 Sorted by residual: bond pdb=" C4' G A 9 " pdb=" O4' G A 9 " ideal model delta sigma weight residual 1.454 1.697 -0.243 1.00e-02 1.00e+04 5.91e+02 bond pdb=" C4' G A 9 " pdb=" C3' G A 9 " ideal model delta sigma weight residual 1.527 1.269 0.258 1.10e-02 8.26e+03 5.51e+02 bond pdb=" N3 G A 9 " pdb=" C4 G A 9 " ideal model delta sigma weight residual 1.350 1.488 -0.138 7.00e-03 2.04e+04 3.88e+02 bond pdb=" C2 G A 9 " pdb=" N3 G A 9 " ideal model delta sigma weight residual 1.323 1.478 -0.155 8.00e-03 1.56e+04 3.77e+02 bond pdb=" C2 G A 9 " pdb=" N2 G A 9 " ideal model delta sigma weight residual 1.341 1.482 -0.141 1.00e-02 1.00e+04 1.99e+02 ... (remaining 4745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.99: 6744 9.99 - 19.97: 8 19.97 - 29.96: 1 29.96 - 39.95: 0 39.95 - 49.93: 1 Bond angle restraints: 6754 Sorted by residual: angle pdb=" C3' G A 9 " pdb=" O3' G A 9 " pdb=" P G A 10 " ideal model delta sigma weight residual 119.70 169.63 -49.93 1.20e+00 6.94e-01 1.73e+03 angle pdb=" C5 G A 9 " pdb=" C6 G A 9 " pdb=" O6 G A 9 " ideal model delta sigma weight residual 128.60 114.35 14.25 6.00e-01 2.78e+00 5.64e+02 angle pdb=" C5 G A 9 " pdb=" C4 G A 9 " pdb=" N3 G A 9 " ideal model delta sigma weight residual 128.60 118.68 9.92 5.00e-01 4.00e+00 3.94e+02 angle pdb=" C5 G A 9 " pdb=" C6 G A 9 " pdb=" N1 G A 9 " ideal model delta sigma weight residual 111.50 121.29 -9.79 5.00e-01 4.00e+00 3.83e+02 angle pdb=" C2 G A 9 " pdb=" N3 G A 9 " pdb=" C4 G A 9 " ideal model delta sigma weight residual 111.90 120.29 -8.39 5.00e-01 4.00e+00 2.82e+02 ... (remaining 6749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.87: 2699 31.87 - 63.74: 249 63.74 - 95.62: 38 95.62 - 127.49: 1 127.49 - 159.36: 1 Dihedral angle restraints: 2988 sinusoidal: 1927 harmonic: 1061 Sorted by residual: dihedral pdb=" C4' G A 9 " pdb=" C3' G A 9 " pdb=" O3' G A 9 " pdb=" P G A 10 " ideal model delta sinusoidal sigma weight residual 250.00 90.64 159.36 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" C4' U A 11 " pdb=" O4' U A 11 " pdb=" C1' U A 11 " pdb=" C2' U A 11 " ideal model delta sinusoidal sigma weight residual -21.00 1.79 -22.79 1 8.00e+00 1.56e-02 1.17e+01 dihedral pdb=" C3' U A 11 " pdb=" C4' U A 11 " pdb=" O4' U A 11 " pdb=" C1' U A 11 " ideal model delta sinusoidal sigma weight residual -2.00 -24.16 22.16 1 8.00e+00 1.56e-02 1.11e+01 ... (remaining 2985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.470: 800 0.470 - 0.940: 0 0.940 - 1.409: 0 1.409 - 1.879: 0 1.879 - 2.349: 1 Chirality restraints: 801 Sorted by residual: chirality pdb=" P G A 9 " pdb=" OP1 G A 9 " pdb=" OP2 G A 9 " pdb=" O5' G A 9 " both_signs ideal model delta sigma weight residual True 2.41 -0.06 2.35 2.00e-01 2.50e+01 1.38e+02 chirality pdb=" C3' AN6 A 101 " pdb=" C2' AN6 A 101 " pdb=" C4' AN6 A 101 " pdb=" O3' AN6 A 101 " both_signs ideal model delta sigma weight residual False -2.72 -2.41 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA' AN6 A 101 " pdb=" C' AN6 A 101 " pdb=" CB' AN6 A 101 " pdb=" N' AN6 A 101 " both_signs ideal model delta sigma weight residual False 2.36 2.62 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 798 not shown) Planarity restraints: 599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A 66 " -0.036 2.00e-02 2.50e+03 2.38e-02 1.28e+01 pdb=" N1 U A 66 " 0.056 2.00e-02 2.50e+03 pdb=" C2 U A 66 " -0.021 2.00e-02 2.50e+03 pdb=" O2 U A 66 " 0.011 2.00e-02 2.50e+03 pdb=" N3 U A 66 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U A 66 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U A 66 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U A 66 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U A 66 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 63 " 0.016 2.00e-02 2.50e+03 1.18e-02 4.17e+00 pdb=" N9 G A 63 " -0.034 2.00e-02 2.50e+03 pdb=" C8 G A 63 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G A 63 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G A 63 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 63 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G A 63 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G A 63 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G A 63 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G A 63 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G A 63 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 63 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 62 " -0.015 2.00e-02 2.50e+03 1.12e-02 3.78e+00 pdb=" N9 G A 62 " 0.031 2.00e-02 2.50e+03 pdb=" C8 G A 62 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A 62 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G A 62 " -0.006 2.00e-02 2.50e+03 pdb=" C6 G A 62 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G A 62 " 0.001 2.00e-02 2.50e+03 pdb=" N1 G A 62 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A 62 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G A 62 " 0.005 2.00e-02 2.50e+03 pdb=" N3 G A 62 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G A 62 " -0.014 2.00e-02 2.50e+03 ... (remaining 596 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 409 2.74 - 3.28: 4792 3.28 - 3.82: 8459 3.82 - 4.36: 9730 4.36 - 4.90: 13985 Nonbonded interactions: 37375 Sorted by model distance: nonbonded pdb=" N2 G A 10 " pdb=" O2 C A 45 " model vdw 2.196 3.120 nonbonded pdb=" CE LYS B 211 " pdb=" N1 AN6 A 101 " model vdw 2.247 3.520 nonbonded pdb=" OG1 THR B 248 " pdb=" O' AN6 A 101 " model vdw 2.260 3.040 nonbonded pdb=" O6 G A 9 " pdb=" O3' AN6 A 101 " model vdw 2.328 3.040 nonbonded pdb=" O4 U A 52 " pdb=" N7 A A 56 " model vdw 2.366 2.496 ... (remaining 37370 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 'B' selection = (chain 'C' and resid 94 through 264) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.550 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 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 : 0.010 0.258 4751 Z= 0.862 Angle : 1.190 49.934 6754 Z= 0.995 Chirality : 0.102 2.349 801 Planarity : 0.004 0.024 599 Dihedral : 21.247 159.358 2298 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.85 % Allowed : 11.27 % Favored : 87.89 % Rotamer: Outliers : 2.42 % Allowed : 17.27 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.43 (0.47), residues: 355 helix: 1.24 (0.51), residues: 115 sheet: -2.99 (1.22), residues: 20 loop : -2.09 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 202 TYR 0.011 0.002 TYR B 123 PHE 0.019 0.002 PHE B 163 TRP 0.012 0.003 TRP B 160 HIS 0.004 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.01043 / 0.86 ( 4750) covalent geometry : angle 1.18985 / 1.00 ( 6754) hydrogen bonds : bond 0.11359 / 12.78 ( 135) hydrogen bonds : angle 6.33293 / 7.79 ( 331) Misc. bond : bond 0.02968 / 1.48 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.138 Fit side-chains REVERT: B 107 MET cc_start: 0.2810 (mpp) cc_final: 0.2551 (mpp) REVERT: B 254 LEU cc_start: 0.8601 (mt) cc_final: 0.8385 (mt) REVERT: C 107 MET cc_start: 0.1129 (OUTLIER) cc_final: 0.0799 (pp-130) REVERT: C 146 GLN cc_start: 0.9481 (mp10) cc_final: 0.9275 (mp10) REVERT: C 225 MET cc_start: 0.1190 (ptm) cc_final: 0.0472 (ppp) outliers start: 8 outliers final: 1 residues processed: 44 average time/residue: 0.0439 time to fit residues: 2.9143 Evaluate side-chains 30 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.0040 chunk 37 optimal weight: 0.0270 overall best weight: 0.4452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN C 161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.135463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.115551 restraints weight = 35235.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.117813 restraints weight = 25295.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.119203 restraints weight = 20410.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.120651 restraints weight = 17570.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.121236 restraints weight = 15702.716| |-----------------------------------------------------------------------------| r_work (final): 0.4638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5214 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4751 Z= 0.135 Angle : 0.657 9.701 6754 Z= 0.341 Chirality : 0.043 0.291 801 Planarity : 0.004 0.025 599 Dihedral : 21.044 130.716 1525 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 1.13 % Allowed : 12.11 % Favored : 86.76 % Rotamer: Outliers : 3.94 % Allowed : 20.30 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.29 (0.47), residues: 355 helix: 1.42 (0.52), residues: 111 sheet: -3.49 (1.73), residues: 10 loop : -2.03 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 202 TYR 0.013 0.002 TYR C 157 PHE 0.011 0.001 PHE C 259 TRP 0.006 0.001 TRP C 264 HIS 0.010 0.002 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 ( 4750) covalent geometry : angle 0.65659 / 0.34 ( 6754) hydrogen bonds : bond 0.04974 / 5.05 ( 135) hydrogen bonds : angle 5.27930 / 6.56 ( 331) Misc. bond : bond 0.00320 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.146 Fit side-chains REVERT: B 107 MET cc_start: 0.2902 (mpp) cc_final: 0.2684 (mpp) REVERT: B 254 LEU cc_start: 0.8738 (mt) cc_final: 0.8531 (mt) REVERT: C 107 MET cc_start: 0.1347 (OUTLIER) cc_final: 0.1030 (pp-130) REVERT: C 225 MET cc_start: 0.0832 (ptm) cc_final: 0.0220 (ppp) outliers start: 13 outliers final: 9 residues processed: 36 average time/residue: 0.0438 time to fit residues: 2.4287 Evaluate side-chains 35 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 40.0000 chunk 19 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN C 161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.130499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.109830 restraints weight = 35932.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.112322 restraints weight = 26580.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.113921 restraints weight = 21839.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.115080 restraints weight = 19030.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.115903 restraints weight = 17126.157| |-----------------------------------------------------------------------------| r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5495 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4751 Z= 0.163 Angle : 0.657 10.583 6754 Z= 0.343 Chirality : 0.042 0.243 801 Planarity : 0.004 0.032 599 Dihedral : 21.120 128.259 1525 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 1.41 % Allowed : 12.68 % Favored : 85.92 % Rotamer: Outliers : 4.85 % Allowed : 21.82 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.65 (0.45), residues: 355 helix: 0.81 (0.49), residues: 117 sheet: -3.52 (1.78), residues: 10 loop : -2.18 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 147 TYR 0.019 0.003 TYR C 157 PHE 0.022 0.002 PHE B 163 TRP 0.014 0.002 TRP C 160 HIS 0.010 0.002 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 ( 4750) covalent geometry : angle 0.65699 / 0.34 ( 6754) hydrogen bonds : bond 0.04916 / 4.92 ( 135) hydrogen bonds : angle 5.26750 / 6.58 ( 331) Misc. bond : bond 0.00632 / 0.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 25 time to evaluate : 0.143 Fit side-chains REVERT: B 107 MET cc_start: 0.3103 (mpp) cc_final: 0.2871 (mpp) REVERT: B 185 TYR cc_start: 0.7185 (t80) cc_final: 0.6860 (t80) REVERT: B 254 LEU cc_start: 0.8916 (mt) cc_final: 0.8646 (mt) REVERT: C 107 MET cc_start: 0.1241 (OUTLIER) cc_final: 0.0441 (pp-130) REVERT: C 163 PHE cc_start: 0.8540 (t80) cc_final: 0.7973 (m-80) REVERT: C 225 MET cc_start: 0.1185 (ptm) cc_final: 0.0621 (ppp) outliers start: 16 outliers final: 12 residues processed: 37 average time/residue: 0.0445 time to fit residues: 2.5058 Evaluate side-chains 36 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 23 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 160 TRP Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 6 optimal weight: 40.0000 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS C 253 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.128200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.107786 restraints weight = 35672.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.110097 restraints weight = 26555.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.111831 restraints weight = 21852.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.112996 restraints weight = 18885.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.113818 restraints weight = 16910.042| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5528 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4751 Z= 0.150 Angle : 0.637 10.658 6754 Z= 0.331 Chirality : 0.040 0.221 801 Planarity : 0.004 0.032 599 Dihedral : 21.357 124.073 1525 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 1.41 % Allowed : 12.11 % Favored : 86.48 % Rotamer: Outliers : 5.45 % Allowed : 23.03 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.78 (0.45), residues: 355 helix: 0.59 (0.49), residues: 117 sheet: -3.64 (1.81), residues: 10 loop : -2.17 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 230 TYR 0.018 0.002 TYR C 157 PHE 0.018 0.002 PHE B 163 TRP 0.012 0.002 TRP C 160 HIS 0.009 0.002 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 ( 4750) covalent geometry : angle 0.63713 / 0.33 ( 6754) hydrogen bonds : bond 0.04369 / 4.32 ( 135) hydrogen bonds : angle 5.22930 / 6.56 ( 331) Misc. bond : bond 0.00393 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 26 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: B 107 MET cc_start: 0.3417 (mpp) cc_final: 0.3188 (mpp) REVERT: B 185 TYR cc_start: 0.7479 (t80) cc_final: 0.7117 (t80) REVERT: B 254 LEU cc_start: 0.8960 (mt) cc_final: 0.8641 (mt) REVERT: C 163 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7986 (m-80) REVERT: C 201 MET cc_start: 0.4213 (mmt) cc_final: 0.3952 (mmm) REVERT: C 225 MET cc_start: 0.1438 (ptm) cc_final: 0.0830 (ppp) outliers start: 18 outliers final: 13 residues processed: 37 average time/residue: 0.0438 time to fit residues: 2.5151 Evaluate side-chains 39 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 256 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 0.0870 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 4 optimal weight: 10.0000 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 131 HIS C 162 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.130478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.110110 restraints weight = 35388.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.112523 restraints weight = 26383.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.114229 restraints weight = 21618.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.115373 restraints weight = 18663.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.115697 restraints weight = 16757.905| |-----------------------------------------------------------------------------| r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5450 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4751 Z= 0.108 Angle : 0.591 10.092 6754 Z= 0.306 Chirality : 0.039 0.214 801 Planarity : 0.004 0.035 599 Dihedral : 21.266 127.134 1525 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 1.41 % Allowed : 12.11 % Favored : 86.48 % Rotamer: Outliers : 5.76 % Allowed : 23.03 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.62 (0.46), residues: 355 helix: 0.72 (0.50), residues: 117 sheet: -3.68 (1.78), residues: 10 loop : -2.07 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 231 TYR 0.015 0.002 TYR C 157 PHE 0.010 0.001 PHE C 148 TRP 0.006 0.001 TRP C 264 HIS 0.008 0.002 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.11 ( 4750) covalent geometry : angle 0.59131 / 0.31 ( 6754) hydrogen bonds : bond 0.03659 / 3.60 ( 135) hydrogen bonds : angle 4.90218 / 6.22 ( 331) Misc. bond : bond 0.00431 / 0.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 25 time to evaluate : 0.149 Fit side-chains REVERT: B 107 MET cc_start: 0.3410 (mpp) cc_final: 0.3179 (mpp) REVERT: B 185 TYR cc_start: 0.7547 (t80) cc_final: 0.7198 (t80) REVERT: B 254 LEU cc_start: 0.8915 (mt) cc_final: 0.8553 (mt) REVERT: C 163 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: C 225 MET cc_start: 0.1263 (ptm) cc_final: 0.0648 (ppp) outliers start: 19 outliers final: 16 residues processed: 37 average time/residue: 0.0454 time to fit residues: 2.5511 Evaluate side-chains 41 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 24 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 160 TRP Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 237 TYR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 256 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 0.0470 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.127584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.107256 restraints weight = 36010.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.109578 restraints weight = 26784.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.111278 restraints weight = 22027.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.112385 restraints weight = 19092.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.112781 restraints weight = 17139.461| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5619 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4751 Z= 0.133 Angle : 0.605 9.567 6754 Z= 0.314 Chirality : 0.040 0.219 801 Planarity : 0.004 0.032 599 Dihedral : 21.375 129.710 1524 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 1.41 % Allowed : 12.68 % Favored : 85.92 % Rotamer: Outliers : 5.15 % Allowed : 24.55 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.71 (0.45), residues: 355 helix: 0.60 (0.48), residues: 117 sheet: -3.81 (1.72), residues: 10 loop : -2.09 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 230 TYR 0.017 0.002 TYR C 157 PHE 0.016 0.002 PHE B 163 TRP 0.007 0.002 TRP C 160 HIS 0.009 0.002 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 4750) covalent geometry : angle 0.60480 / 0.31 ( 6754) hydrogen bonds : bond 0.04175 / 4.07 ( 135) hydrogen bonds : angle 4.95975 / 6.30 ( 331) Misc. bond : bond 0.00327 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 23 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: B 185 TYR cc_start: 0.7804 (t80) cc_final: 0.7373 (t80) REVERT: B 254 LEU cc_start: 0.9000 (mt) cc_final: 0.8691 (mt) REVERT: C 163 PHE cc_start: 0.8629 (t80) cc_final: 0.8017 (m-80) REVERT: C 225 MET cc_start: 0.1577 (ptm) cc_final: 0.0963 (ppp) outliers start: 17 outliers final: 16 residues processed: 34 average time/residue: 0.0436 time to fit residues: 2.3053 Evaluate side-chains 39 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 23 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 160 TRP Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 256 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 6 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 34 optimal weight: 0.0670 chunk 10 optimal weight: 0.9980 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.126967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.106900 restraints weight = 35391.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.108661 restraints weight = 26347.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.110704 restraints weight = 21665.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.111595 restraints weight = 18808.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.112543 restraints weight = 17017.327| |-----------------------------------------------------------------------------| r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4751 Z= 0.120 Angle : 0.589 9.119 6754 Z= 0.306 Chirality : 0.039 0.235 801 Planarity : 0.004 0.034 599 Dihedral : 21.502 130.570 1524 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 1.41 % Allowed : 13.24 % Favored : 85.35 % Rotamer: Outliers : 6.36 % Allowed : 23.33 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.75 (0.45), residues: 355 helix: 0.57 (0.48), residues: 117 sheet: -3.85 (1.71), residues: 10 loop : -2.11 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 202 TYR 0.015 0.002 TYR C 157 PHE 0.011 0.001 PHE B 163 TRP 0.006 0.002 TRP C 264 HIS 0.007 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 ( 4750) covalent geometry : angle 0.58879 / 0.31 ( 6754) hydrogen bonds : bond 0.03750 / 3.66 ( 135) hydrogen bonds : angle 4.86084 / 6.10 ( 331) Misc. bond : bond 0.00360 / 0.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 23 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 185 TYR cc_start: 0.7884 (t80) cc_final: 0.7476 (t80) REVERT: B 254 LEU cc_start: 0.8989 (mt) cc_final: 0.8680 (mt) REVERT: C 163 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8074 (m-80) REVERT: C 225 MET cc_start: 0.1488 (ptm) cc_final: 0.0912 (ppp) outliers start: 21 outliers final: 18 residues processed: 38 average time/residue: 0.0574 time to fit residues: 3.0172 Evaluate side-chains 42 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 23 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 160 TRP Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 256 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.126165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.106141 restraints weight = 36334.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.108708 restraints weight = 26367.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.110317 restraints weight = 21397.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.111412 restraints weight = 18475.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.112026 restraints weight = 16552.304| |-----------------------------------------------------------------------------| r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5680 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4751 Z= 0.111 Angle : 0.581 8.666 6754 Z= 0.303 Chirality : 0.039 0.260 801 Planarity : 0.004 0.032 599 Dihedral : 21.508 132.394 1524 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 1.41 % Allowed : 11.83 % Favored : 86.76 % Rotamer: Outliers : 5.76 % Allowed : 26.06 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.62 (0.45), residues: 355 helix: 0.67 (0.49), residues: 117 sheet: -3.76 (1.73), residues: 10 loop : -2.03 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 127 TYR 0.015 0.002 TYR C 157 PHE 0.010 0.001 PHE C 148 TRP 0.006 0.001 TRP C 160 HIS 0.007 0.002 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 4750) covalent geometry : angle 0.58142 / 0.30 ( 6754) hydrogen bonds : bond 0.03611 / 3.51 ( 135) hydrogen bonds : angle 4.76729 / 5.97 ( 331) Misc. bond : bond 0.00321 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 24 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 185 TYR cc_start: 0.8029 (t80) cc_final: 0.7494 (t80) REVERT: B 254 LEU cc_start: 0.9058 (mt) cc_final: 0.8758 (mt) REVERT: C 163 PHE cc_start: 0.8731 (t80) cc_final: 0.8141 (m-80) REVERT: C 225 MET cc_start: 0.1645 (ptm) cc_final: 0.1061 (ppp) outliers start: 19 outliers final: 18 residues processed: 37 average time/residue: 0.0512 time to fit residues: 2.7555 Evaluate side-chains 42 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 24 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 160 TRP Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 256 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 40.0000 chunk 33 optimal weight: 0.0270 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.124057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.104052 restraints weight = 36050.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.106309 restraints weight = 26733.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.107658 restraints weight = 21956.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.108966 restraints weight = 19051.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.109701 restraints weight = 16976.433| |-----------------------------------------------------------------------------| r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5700 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4751 Z= 0.139 Angle : 0.612 8.470 6754 Z= 0.318 Chirality : 0.040 0.273 801 Planarity : 0.004 0.039 599 Dihedral : 21.624 133.385 1524 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 1.41 % Allowed : 14.65 % Favored : 83.94 % Rotamer: Outliers : 5.76 % Allowed : 25.45 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.75 (0.45), residues: 355 helix: 0.67 (0.48), residues: 111 sheet: -3.82 (1.74), residues: 10 loop : -2.11 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 231 TYR 0.014 0.002 TYR C 157 PHE 0.014 0.002 PHE B 163 TRP 0.008 0.002 TRP C 160 HIS 0.008 0.002 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 4750) covalent geometry : angle 0.61150 / 0.32 ( 6754) hydrogen bonds : bond 0.04116 / 4.05 ( 135) hydrogen bonds : angle 4.85772 / 6.05 ( 331) Misc. bond : bond 0.00237 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 23 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: B 254 LEU cc_start: 0.9058 (mt) cc_final: 0.8669 (mt) REVERT: C 91 THR cc_start: 0.4179 (OUTLIER) cc_final: 0.3975 (p) REVERT: C 163 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8149 (m-80) REVERT: C 225 MET cc_start: 0.1773 (ptm) cc_final: 0.1143 (ppp) outliers start: 19 outliers final: 16 residues processed: 36 average time/residue: 0.0432 time to fit residues: 2.4140 Evaluate side-chains 41 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 23 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 160 TRP Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 2 optimal weight: 30.0000 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 5 optimal weight: 40.0000 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 30.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.123778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.103867 restraints weight = 36183.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.105800 restraints weight = 26795.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.107572 restraints weight = 21943.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.108035 restraints weight = 18981.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.109209 restraints weight = 17598.409| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5720 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4751 Z= 0.131 Angle : 0.619 8.762 6754 Z= 0.321 Chirality : 0.040 0.271 801 Planarity : 0.004 0.033 599 Dihedral : 21.683 133.297 1524 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 1.41 % Allowed : 12.96 % Favored : 85.63 % Rotamer: Outliers : 5.76 % Allowed : 25.76 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.86 (0.45), residues: 355 helix: 0.70 (0.49), residues: 111 sheet: -4.11 (1.58), residues: 10 loop : -2.24 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 230 TYR 0.014 0.002 TYR C 157 PHE 0.013 0.002 PHE B 163 TRP 0.008 0.002 TRP C 160 HIS 0.007 0.002 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 4750) covalent geometry : angle 0.61939 / 0.32 ( 6754) hydrogen bonds : bond 0.03894 / 3.91 ( 135) hydrogen bonds : angle 4.84046 / 5.99 ( 331) Misc. bond : bond 0.00254 / 0.13 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 23 time to evaluate : 0.146 Fit side-chains REVERT: B 185 TYR cc_start: 0.7835 (t80) cc_final: 0.7507 (t80) REVERT: B 254 LEU cc_start: 0.9031 (mt) cc_final: 0.8625 (mt) REVERT: C 163 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8151 (m-80) REVERT: C 225 MET cc_start: 0.1826 (ptm) cc_final: 0.1215 (ppp) outliers start: 19 outliers final: 16 residues processed: 36 average time/residue: 0.0388 time to fit residues: 2.1908 Evaluate side-chains 40 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 23 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 160 TRP Chi-restraints excluded: chain C residue 163 PHE Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 40.0000 chunk 12 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.124558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.104606 restraints weight = 36916.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.106599 restraints weight = 26792.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.108606 restraints weight = 21786.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.109117 restraints weight = 18609.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.110377 restraints weight = 17139.968| |-----------------------------------------------------------------------------| r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5691 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4751 Z= 0.109 Angle : 0.591 8.217 6754 Z= 0.307 Chirality : 0.039 0.269 801 Planarity : 0.004 0.035 599 Dihedral : 21.658 132.776 1524 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 1.41 % Allowed : 13.24 % Favored : 85.35 % Rotamer: Outliers : 5.15 % Allowed : 26.67 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -1.97 (0.44), residues: 355 helix: 0.19 (0.48), residues: 123 sheet: -3.77 (1.72), residues: 10 loop : -2.20 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 TYR 0.016 0.002 TYR C 157 PHE 0.013 0.002 PHE C 148 TRP 0.007 0.001 TRP C 160 HIS 0.006 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 4750) covalent geometry : angle 0.59130 / 0.31 ( 6754) hydrogen bonds : bond 0.03351 / 3.40 ( 135) hydrogen bonds : angle 4.67795 / 5.81 ( 331) Misc. bond : bond 0.00255 / 0.13 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1305.80 seconds wall clock time: 23 minutes 6.58 seconds (1386.58 seconds total)