Starting phenix.real_space_refine on Thu Jul 2 00:18:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xzs_72370/07_2026/9xzs_72370_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xzs_72370/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9xzs_72370/07_2026/9xzs_72370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xzs_72370/07_2026/9xzs_72370.map" model { file = "/net/cci-nas-00/data/ceres_data/9xzs_72370/07_2026/9xzs_72370_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xzs_72370/07_2026/9xzs_72370_neut.cif" } 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-dev-6108/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: 0.99, per 1000 atoms: 0.22 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: 0.34 Conformation dependent library (CDL) restraints added in 124.6 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: 0.49 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: 0.70 Time building geometry restraints manager: 0.47 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=" 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=" C4' G A 9 " pdb=" C3' G A 9 " ideal model delta sigma weight residual 1.527 1.269 0.258 1.50e-02 4.44e+03 2.96e+02 bond pdb=" C4' G A 9 " pdb=" O4' G A 9 " ideal model delta sigma weight residual 1.454 1.697 -0.243 1.50e-02 4.44e+03 2.62e+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 - 9.89: 6743 9.89 - 19.77: 9 19.77 - 29.66: 1 29.66 - 39.55: 0 39.55 - 49.43: 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 120.20 169.63 -49.43 1.50e+00 4.44e-01 1.09e+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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.320 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.040 ------------------------------------------------------------------------------- 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= 0.769 Angle : 1.124 49.434 6754 Z= 0.895 Chirality : 0.095 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 0.01040 / 0.77 ( 4750) covalent geometry : angle 1.12418 / 0.89 ( 6754) hydrogen bonds : bond 0.11359 / 11.78 ( 135) hydrogen bonds : angle 6.33293 / 7.14 ( 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 : 0.135 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: 0.0390 time to fit residues: 2.5535 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 : 0.104 ------------------------------------------------------------------------------- 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: 20.0000 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: 0.3980 chunk 22 optimal weight: 0.0040 chunk 37 optimal weight: 0.0270 overall best weight: 0.3250 ------------------------------------------------------------------------------- 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 = 0.135507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.115074 restraints weight = 35305.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.117306 restraints weight = 25732.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.119378 restraints weight = 20786.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.120615 restraints weight = 17792.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.121480 restraints weight = 15859.865| |-----------------------------------------------------------------------------| r_work (final): 0.4630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5199 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4751 Z= 0.134 Angle : 0.642 9.585 6754 Z= 0.337 Chirality : 0.041 0.278 801 Planarity : 0.004 0.024 599 Dihedral : 21.099 132.453 1525 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 1.13 % Allowed : 11.83 % Favored : 87.04 % 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: -1.43 (0.47), residues: 355 helix: 1.43 (0.52), residues: 111 sheet: -3.11 (1.25), residues: 20 loop : -2.14 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 231 TYR 0.012 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 0.00262 / 0.13 ( 4750) covalent geometry : angle 0.64190 / 0.34 ( 6754) hydrogen bonds : bond 0.05026 / 4.86 ( 135) hydrogen bonds : angle 5.32260 / 6.04 ( 331) Misc. bond : bond 0.00558 / 0.28 ( 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: 0.2909 (mpp) cc_final: 0.2680 (mpp) REVERT: B 254 LEU cc_start: 0.8723 (mt) cc_final: 0.8516 (mt) REVERT: C 107 MET cc_start: 0.1468 (OUTLIER) cc_final: 0.1173 (pp-130) REVERT: C 225 MET cc_start: 0.0915 (ptm) cc_final: 0.0272 (ppp) outliers start: 13 outliers final: 9 residues processed: 36 average time/residue: 0.0445 time to fit residues: 2.4970 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 : 0.134 ------------------------------------------------------------------------------- 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: 20.0000 chunk 34 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.131659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.110890 restraints weight = 35853.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.113466 restraints weight = 26615.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.115132 restraints weight = 21779.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.116272 restraints weight = 18906.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.116673 restraints weight = 16985.230| |-----------------------------------------------------------------------------| r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4751 Z= 0.152 Angle : 0.636 10.233 6754 Z= 0.337 Chirality : 0.040 0.242 801 Planarity : 0.004 0.031 599 Dihedral : 21.149 127.964 1525 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 1.41 % Allowed : 11.55 % Favored : 87.04 % Rotamer: Outliers : 4.55 % Allowed : 22.12 % 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: -1.67 (0.46), residues: 355 helix: 0.94 (0.50), residues: 117 sheet: -1.66 (1.19), residues: 30 loop : -2.38 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 147 TYR 0.019 0.002 TYR B 185 PHE 0.019 0.002 PHE B 163 TRP 0.015 0.002 TRP C 160 HIS 0.010 0.002 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 ( 4750) covalent geometry : angle 0.63578 / 0.34 ( 6754) hydrogen bonds : bond 0.04690 / 4.46 ( 135) hydrogen bonds : angle 5.19698 / 5.94 ( 331) Misc. bond : bond 0.00046 / 0.02 ( 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 40 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.082 Fit side-chains REVERT: B 107 MET cc_start: 0.3051 (mpp) cc_final: 0.2845 (mpp) REVERT: B 185 TYR cc_start: 0.7148 (t80) cc_final: 0.6892 (t80) REVERT: B 254 LEU cc_start: 0.8883 (mt) cc_final: 0.8545 (mt) REVERT: C 107 MET cc_start: 0.1423 (OUTLIER) cc_final: 0.0263 (pp-130) REVERT: C 163 PHE cc_start: 0.8474 (t80) cc_final: 0.7896 (m-80) REVERT: C 201 MET cc_start: 0.3588 (mmt) cc_final: 0.3355 (mmm) REVERT: C 225 MET cc_start: 0.1080 (ptm) cc_final: 0.0521 (ppp) outliers start: 15 outliers final: 11 residues processed: 36 average time/residue: 0.0432 time to fit residues: 2.3318 Evaluate side-chains 35 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 overall best weight: 2.5184 ------------------------------------------------------------------------------- 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 = 0.4745 r_free = 0.4745 target = 0.128583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.108162 restraints weight = 35602.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.110279 restraints weight = 26521.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.112204 restraints weight = 21881.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.113350 restraints weight = 18877.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.114144 restraints weight = 16927.059| |-----------------------------------------------------------------------------| r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5574 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4751 Z= 0.152 Angle : 0.624 10.490 6754 Z= 0.330 Chirality : 0.039 0.222 801 Planarity : 0.004 0.031 599 Dihedral : 21.332 126.137 1525 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 1.41 % Allowed : 12.39 % Favored : 86.20 % 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: -1.69 (0.45), residues: 355 helix: 0.59 (0.49), residues: 117 sheet: -3.65 (1.79), residues: 10 loop : -2.07 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 230 TYR 0.017 0.002 TYR C 157 PHE 0.019 0.002 PHE B 163 TRP 0.011 0.002 TRP C 160 HIS 0.009 0.002 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 ( 4750) covalent geometry : angle 0.62449 / 0.33 ( 6754) hydrogen bonds : bond 0.04374 / 4.09 ( 135) hydrogen bonds : angle 5.21838 / 5.95 ( 331) Misc. bond : bond 0.00442 / 0.22 ( 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 : 0.133 Fit side-chains revert: symmetry clash REVERT: B 107 MET cc_start: 0.3407 (mpp) cc_final: 0.3181 (mpp) REVERT: B 185 TYR cc_start: 0.7583 (t80) cc_final: 0.7212 (t80) REVERT: B 254 LEU cc_start: 0.8981 (mt) cc_final: 0.8675 (mt) REVERT: C 163 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: C 225 MET cc_start: 0.1539 (ptm) cc_final: 0.0907 (ppp) outliers start: 18 outliers final: 13 residues processed: 37 average time/residue: 0.0377 time to fit residues: 2.1788 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 : 0.081 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 0.0010 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 20.0000 chunk 4 optimal weight: 11.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- 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 = 0.4758 r_free = 0.4758 target = 0.129547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.109210 restraints weight = 35568.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.111447 restraints weight = 26597.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.113185 restraints weight = 21913.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.114408 restraints weight = 18901.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.115197 restraints weight = 16864.444| |-----------------------------------------------------------------------------| r_work (final): 0.4540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5509 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4751 Z= 0.116 Angle : 0.588 10.050 6754 Z= 0.308 Chirality : 0.038 0.210 801 Planarity : 0.004 0.036 599 Dihedral : 21.299 127.433 1525 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 1.41 % Allowed : 11.83 % Favored : 86.76 % Rotamer: Outliers : 6.06 % Allowed : 23.33 % Favored : 70.61 % 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: -1.63 (0.46), residues: 355 helix: 0.75 (0.50), residues: 117 sheet: -3.68 (1.77), residues: 10 loop : -2.09 (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 0.008 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 0.00228 / 0.12 ( 4750) covalent geometry : angle 0.58825 / 0.31 ( 6754) hydrogen bonds : bond 0.03624 / 3.31 ( 135) hydrogen bonds : angle 4.96109 / 5.70 ( 331) Misc. bond : bond 0.00442 / 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 45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 25 time to evaluate : 0.083 Fit side-chains REVERT: B 107 MET cc_start: 0.3328 (mpp) cc_final: 0.3105 (mpp) REVERT: B 185 TYR cc_start: 0.7618 (t80) cc_final: 0.7250 (t80) REVERT: B 254 LEU cc_start: 0.8953 (mt) cc_final: 0.8661 (mt) REVERT: C 163 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: C 225 MET cc_start: 0.1489 (ptm) cc_final: 0.0864 (ppp) outliers start: 20 outliers final: 17 residues processed: 38 average time/residue: 0.0384 time to fit residues: 2.2187 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 : 0.136 ------------------------------------------------------------------------------- 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 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 237 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 0.0170 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.5024 ------------------------------------------------------------------------------- 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 = 0.4737 r_free = 0.4737 target = 0.127958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.107977 restraints weight = 35846.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.110161 restraints weight = 26751.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.111841 restraints weight = 21954.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.112956 restraints weight = 19043.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.113812 restraints weight = 16976.442| |-----------------------------------------------------------------------------| r_work (final): 0.4520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5545 moved from start: 0.2228 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= 0.119 Angle : 0.600 9.501 6754 Z= 0.312 Chirality : 0.038 0.188 801 Planarity : 0.004 0.033 599 Dihedral : 21.320 130.189 1525 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 1.41 % Allowed : 12.11 % Favored : 86.48 % Rotamer: Outliers : 5.15 % Allowed : 24.85 % Favored : 70.00 % 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: 0.69 (0.49), residues: 117 sheet: -3.70 (1.75), residues: 10 loop : -2.08 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 202 TYR 0.016 0.002 TYR C 157 PHE 0.012 0.001 PHE B 163 TRP 0.006 0.001 TRP C 160 HIS 0.009 0.002 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 4750) covalent geometry : angle 0.60034 / 0.31 ( 6754) hydrogen bonds : bond 0.03828 / 3.48 ( 135) hydrogen bonds : angle 4.91197 / 5.70 ( 331) Misc. bond : bond 0.00379 / 0.19 ( 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 : 0.137 Fit side-chains REVERT: B 107 MET cc_start: 0.3396 (mpp) cc_final: 0.3168 (mpp) REVERT: B 185 TYR cc_start: 0.7760 (t80) cc_final: 0.7396 (t80) REVERT: B 230 ARG cc_start: 0.5170 (OUTLIER) cc_final: 0.4542 (mpt90) REVERT: B 254 LEU cc_start: 0.8978 (mt) cc_final: 0.8674 (mt) REVERT: C 163 PHE cc_start: 0.8650 (t80) cc_final: 0.8025 (m-80) REVERT: C 225 MET cc_start: 0.1560 (ptm) cc_final: 0.0907 (ppp) outliers start: 17 outliers final: 14 residues processed: 35 average time/residue: 0.0512 time to fit residues: 2.5486 Evaluate side-chains 38 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 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 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 160 TRP 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: 5.9990 chunk 21 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 18 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 6 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 34 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- 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 = 0.4743 r_free = 0.4743 target = 0.128653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.109224 restraints weight = 35583.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.111247 restraints weight = 26608.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.113013 restraints weight = 21727.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.114113 restraints weight = 18792.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.114903 restraints weight = 16824.340| |-----------------------------------------------------------------------------| r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 0.2292 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= 0.103 Angle : 0.573 9.193 6754 Z= 0.299 Chirality : 0.038 0.189 801 Planarity : 0.004 0.034 599 Dihedral : 21.320 130.374 1524 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 1.41 % Allowed : 12.68 % Favored : 85.92 % Rotamer: Outliers : 5.15 % Allowed : 25.45 % Favored : 69.39 % 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: -1.58 (0.45), residues: 355 helix: 0.80 (0.49), residues: 117 sheet: -3.66 (1.73), residues: 10 loop : -2.07 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 202 TYR 0.015 0.002 TYR C 157 PHE 0.009 0.001 PHE C 148 TRP 0.006 0.001 TRP C 160 HIS 0.006 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 ( 4750) covalent geometry : angle 0.57328 / 0.30 ( 6754) hydrogen bonds : bond 0.03416 / 3.07 ( 135) hydrogen bonds : angle 4.70541 / 5.42 ( 331) Misc. bond : bond 0.00354 / 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 42 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 185 TYR cc_start: 0.7725 (t80) cc_final: 0.7371 (t80) REVERT: B 254 LEU cc_start: 0.8955 (mt) cc_final: 0.8592 (mt) REVERT: C 163 PHE cc_start: 0.8644 (t80) cc_final: 0.8043 (m-80) REVERT: C 225 MET cc_start: 0.1234 (ptm) cc_final: 0.0645 (ppp) outliers start: 17 outliers final: 16 residues processed: 36 average time/residue: 0.0388 time to fit residues: 1.9585 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 : 0.130 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 8.9990 chunk 6 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 32 optimal weight: 0.0670 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 2.6124 ------------------------------------------------------------------------------- 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 = 0.4689 r_free = 0.4689 target = 0.124767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.104785 restraints weight = 36383.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.106721 restraints weight = 27093.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.108504 restraints weight = 22127.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.109341 restraints weight = 19126.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.110379 restraints weight = 17219.997| |-----------------------------------------------------------------------------| r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5692 moved from start: 0.2771 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= 0.154 Angle : 0.615 8.842 6754 Z= 0.326 Chirality : 0.040 0.171 801 Planarity : 0.005 0.049 599 Dihedral : 21.539 132.089 1524 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 1.41 % Allowed : 13.52 % Favored : 85.07 % Rotamer: Outliers : 5.76 % Allowed : 24.24 % Favored : 70.00 % 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: -1.68 (0.45), residues: 355 helix: 0.71 (0.49), residues: 111 sheet: -3.82 (1.76), residues: 10 loop : -2.05 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 202 TYR 0.014 0.002 TYR C 157 PHE 0.019 0.002 PHE B 163 TRP 0.009 0.002 TRP C 160 HIS 0.008 0.002 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 4750) covalent geometry : angle 0.61513 / 0.33 ( 6754) hydrogen bonds : bond 0.04374 / 4.05 ( 135) hydrogen bonds : angle 4.93637 / 5.68 ( 331) Misc. bond : bond 0.00235 / 0.12 ( 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 42 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 23 time to evaluate : 0.120 Fit side-chains REVERT: B 185 TYR cc_start: 0.7963 (t80) cc_final: 0.7497 (t80) REVERT: B 254 LEU cc_start: 0.9027 (mt) cc_final: 0.8634 (mt) REVERT: C 163 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8131 (m-80) REVERT: C 225 MET cc_start: 0.1656 (ptm) cc_final: 0.1073 (ppp) outliers start: 19 outliers final: 15 residues processed: 36 average time/residue: 0.0367 time to fit residues: 2.0377 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 : 0.092 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 30.0000 chunk 33 optimal weight: 10.0000 chunk 22 optimal weight: 0.0980 chunk 25 optimal weight: 0.0670 chunk 30 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.8324 ------------------------------------------------------------------------------- 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 = 0.4698 r_free = 0.4698 target = 0.125246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.105626 restraints weight = 35793.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.107482 restraints weight = 26599.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.109157 restraints weight = 21763.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.110254 restraints weight = 18871.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.110589 restraints weight = 16959.893| |-----------------------------------------------------------------------------| r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4751 Z= 0.125 Angle : 0.613 8.919 6754 Z= 0.321 Chirality : 0.039 0.178 801 Planarity : 0.004 0.034 599 Dihedral : 21.618 132.695 1524 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 1.41 % Allowed : 12.96 % Favored : 85.63 % Rotamer: Outliers : 4.85 % Allowed : 25.45 % Favored : 69.70 % 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: -1.72 (0.45), residues: 355 helix: 0.77 (0.49), residues: 111 sheet: -4.00 (1.68), residues: 10 loop : -2.12 (0.41), residues: 234 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 0.011 0.002 PHE B 163 TRP 0.007 0.002 TRP C 160 HIS 0.006 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 ( 4750) covalent geometry : angle 0.61327 / 0.32 ( 6754) hydrogen bonds : bond 0.03700 / 3.38 ( 135) hydrogen bonds : angle 4.81239 / 5.47 ( 331) Misc. bond : bond 0.00314 / 0.16 ( 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 39 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 23 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: B 254 LEU cc_start: 0.9016 (mt) cc_final: 0.8697 (mt) REVERT: C 163 PHE cc_start: 0.8676 (t80) cc_final: 0.8140 (m-80) REVERT: C 225 MET cc_start: 0.1656 (ptm) cc_final: 0.1090 (ppp) outliers start: 16 outliers final: 16 residues processed: 34 average time/residue: 0.0324 time to fit residues: 1.7404 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 : 0.086 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4646 r_free = 0.4646 target = 0.120791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.100975 restraints weight = 36665.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.103106 restraints weight = 26994.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.104434 restraints weight = 22049.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.105679 restraints weight = 19143.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.106275 restraints weight = 17202.398| |-----------------------------------------------------------------------------| r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4751 Z= 0.168 Angle : 0.660 8.460 6754 Z= 0.350 Chirality : 0.041 0.165 801 Planarity : 0.006 0.053 599 Dihedral : 21.899 135.335 1524 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 1.41 % Allowed : 14.93 % Favored : 83.66 % Rotamer: Outliers : 4.85 % Allowed : 26.06 % Favored : 69.09 % 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: -2.23 (0.44), residues: 355 helix: 0.02 (0.48), residues: 118 sheet: -4.59 (1.38), residues: 10 loop : -2.30 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 230 TYR 0.015 0.002 TYR B 123 PHE 0.020 0.003 PHE B 163 TRP 0.010 0.002 TRP C 160 HIS 0.008 0.002 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 ( 4750) covalent geometry : angle 0.66046 / 0.35 ( 6754) hydrogen bonds : bond 0.04846 / 4.61 ( 135) hydrogen bonds : angle 5.07940 / 5.72 ( 331) Misc. bond : bond 0.00170 / 0.09 ( 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 39 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 23 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: B 254 LEU cc_start: 0.9057 (mt) cc_final: 0.8635 (mt) REVERT: C 107 MET cc_start: 0.3981 (OUTLIER) cc_final: 0.3598 (ppp) REVERT: C 163 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: C 225 MET cc_start: 0.1880 (ptm) cc_final: 0.1331 (ppp) outliers start: 16 outliers final: 13 residues processed: 33 average time/residue: 0.0284 time to fit residues: 1.4466 Evaluate side-chains 38 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 23 time to evaluate : 0.079 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 20.0000 chunk 12 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4696 r_free = 0.4696 target = 0.124483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.104787 restraints weight = 36754.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.107153 restraints weight = 26339.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.108851 restraints weight = 21212.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.109739 restraints weight = 18096.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.110082 restraints weight = 16300.664| |-----------------------------------------------------------------------------| r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5699 moved from start: 0.3295 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 : 0.603 8.463 6754 Z= 0.316 Chirality : 0.039 0.162 801 Planarity : 0.004 0.042 599 Dihedral : 21.792 133.899 1524 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 1.41 % Allowed : 13.52 % Favored : 85.07 % Rotamer: Outliers : 3.94 % Allowed : 26.67 % Favored : 69.39 % 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: -2.01 (0.44), residues: 355 helix: 0.15 (0.48), residues: 123 sheet: -4.12 (1.54), residues: 10 loop : -2.20 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 127 TYR 0.016 0.002 TYR C 123 PHE 0.017 0.002 PHE C 148 TRP 0.007 0.001 TRP C 160 HIS 0.005 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 4750) covalent geometry : angle 0.60262 / 0.32 ( 6754) hydrogen bonds : bond 0.03423 / 3.24 ( 135) hydrogen bonds : angle 4.63412 / 5.26 ( 331) Misc. bond : bond 0.00323 / 0.16 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1112.98 seconds wall clock time: 19 minutes 48.46 seconds (1188.46 seconds total)