Starting phenix.real_space_refine on Tue Aug 4 12:54:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xzq_72368/08_2026/9xzq_72368_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xzq_72368/08_2026/9xzq_72368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xzq_72368/08_2026/9xzq_72368_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xzq_72368/08_2026/9xzq_72368_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xzq_72368/08_2026/9xzq_72368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xzq_72368/08_2026/9xzq_72368.map" } resolution = 3.63 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 7 5.16 5 C 1673 2.51 5 N 540 2.21 5 O 799 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: 3090 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1511 Classifications: {'RNA': 71} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 27, 'rna3p_pyr': 30} Link IDs: {'rna2p': 14, 'rna3p': 56} Chain: "B" 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: 0.98, per 1000 atoms: 0.32 Number of scatterers: 3090 At special positions: 0 Unit cell: (53.56, 66.744, 81.576, 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 7 16.00 P 71 15.00 O 799 8.00 N 540 7.00 C 1673 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: 0.32 Conformation dependent library (CDL) restraints added in 63.5 milliseconds 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 362 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 1 sheets defined 47.6% alpha, 9.0% beta 17 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.665A pdb=" N MET B 107 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 128 Processing helix chain 'B' and resid 142 through 152 removed outlier: 3.937A pdb=" N GLN B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 removed outlier: 5.741A pdb=" N TYR B 157 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU B 158 " --> pdb=" O THR B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 216 through 226 Processing helix chain 'B' and resid 247 through 262 removed outlier: 3.595A pdb=" N PHE B 259 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing sheet with id=AA1, first strand: chain 'B' and resid 163 through 165 removed outlier: 6.589A pdb=" N ILE B 135 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE B 97 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU B 96 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL B 205 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE B 98 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL B 184 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N GLY B 206 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N LEU B 186 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ARG B 230 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR B 185 " --> pdb=" O ARG B 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 52 hydrogen bonds defined for protein. 135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 0.46 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 1 1.18 - 1.34: 720 1.34 - 1.49: 1459 1.49 - 1.65: 1104 1.65 - 1.81: 14 Bond restraints: 3298 Sorted by residual: bond pdb=" O3' C A 64 " pdb=" P U A 65 " ideal model delta sigma weight residual 1.607 1.022 0.585 1.20e-02 6.94e+03 2.37e+03 bond pdb=" C4' G A 9 " pdb=" C3' G A 9 " ideal model delta sigma weight residual 1.527 1.266 0.261 1.10e-02 8.26e+03 5.62e+02 bond pdb=" C4' G A 9 " pdb=" O4' G A 9 " ideal model delta sigma weight residual 1.454 1.688 -0.234 1.00e-02 1.00e+04 5.46e+02 bond pdb=" N3 G A 9 " pdb=" C4 G A 9 " ideal model delta sigma weight residual 1.350 1.486 -0.136 7.00e-03 2.04e+04 3.80e+02 bond pdb=" C2 G A 9 " pdb=" N3 G A 9 " ideal model delta sigma weight residual 1.323 1.472 -0.149 8.00e-03 1.56e+04 3.48e+02 ... (remaining 3293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.09: 4790 10.09 - 20.19: 6 20.19 - 30.28: 2 30.28 - 40.37: 1 40.37 - 50.46: 2 Bond angle restraints: 4801 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 119.70 146.93 -27.23 1.20e+00 6.94e-01 5.15e+02 angle pdb=" C5 G A 9 " pdb=" C4 G A 9 " pdb=" N3 G A 9 " ideal model delta sigma weight residual 128.60 119.82 8.78 5.00e-01 4.00e+00 3.08e+02 angle pdb=" C5 G A 9 " pdb=" C6 G A 9 " pdb=" O6 G A 9 " ideal model delta sigma weight residual 128.60 118.12 10.48 6.00e-01 2.78e+00 3.05e+02 angle pdb=" OP1 G A 9 " pdb=" P G A 9 " pdb=" O5' G A 9 " ideal model delta sigma weight residual 108.00 158.46 -50.46 3.00e+00 1.11e-01 2.83e+02 angle pdb=" C5 G A 9 " pdb=" C6 G A 9 " pdb=" N1 G A 9 " ideal model delta sigma weight residual 111.50 119.63 -8.13 5.00e-01 4.00e+00 2.64e+02 ... (remaining 4796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 1897 35.95 - 71.90: 179 71.90 - 107.85: 26 107.85 - 143.80: 0 143.80 - 179.75: 2 Dihedral angle restraints: 2104 sinusoidal: 1548 harmonic: 556 Sorted by residual: dihedral pdb=" C5' G A 9 " pdb=" C4' G A 9 " pdb=" C3' G A 9 " pdb=" O3' G A 9 " ideal model delta sinusoidal sigma weight residual 147.00 83.79 63.21 1 8.00e+00 1.56e-02 8.24e+01 dihedral pdb=" O4' G A 9 " pdb=" C4' G A 9 " pdb=" C3' G A 9 " pdb=" C2' G A 9 " ideal model delta sinusoidal sigma weight residual 24.00 -36.68 60.68 1 8.00e+00 1.56e-02 7.65e+01 dihedral pdb=" C4' G A 9 " pdb=" C3' G A 9 " pdb=" C2' G A 9 " pdb=" C1' G A 9 " ideal model delta sinusoidal sigma weight residual -35.00 21.16 -56.16 1 8.00e+00 1.56e-02 6.65e+01 ... (remaining 2101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.480: 590 0.480 - 0.959: 0 0.959 - 1.439: 0 1.439 - 1.919: 0 1.919 - 2.398: 1 Chirality restraints: 591 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 0.01 2.40 2.00e-01 2.50e+01 1.44e+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 -2.39 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C3' G A 9 " pdb=" C4' G A 9 " pdb=" O3' G A 9 " pdb=" C2' G A 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 588 not shown) Planarity restraints: 349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 28 " -0.029 2.00e-02 2.50e+03 2.30e-02 1.46e+01 pdb=" N9 A A 28 " 0.057 2.00e-02 2.50e+03 pdb=" C8 A A 28 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A A 28 " -0.007 2.00e-02 2.50e+03 pdb=" C5 A A 28 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A A 28 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A A 28 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A A 28 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A A 28 " 0.007 2.00e-02 2.50e+03 pdb=" N3 A A 28 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A A 28 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 27 " -0.034 2.00e-02 2.50e+03 1.99e-02 1.09e+01 pdb=" N9 A A 27 " 0.054 2.00e-02 2.50e+03 pdb=" C8 A A 27 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A A 27 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A A 27 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A A 27 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A A 27 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A A 27 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A A 27 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A A 27 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A A 27 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 66 " 0.023 2.00e-02 2.50e+03 2.06e-02 9.55e+00 pdb=" N1 U A 66 " -0.050 2.00e-02 2.50e+03 pdb=" C2 U A 66 " 0.027 2.00e-02 2.50e+03 pdb=" O2 U A 66 " -0.008 2.00e-02 2.50e+03 pdb=" N3 U A 66 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U A 66 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U A 66 " 0.002 2.00e-02 2.50e+03 pdb=" C5 U A 66 " 0.005 2.00e-02 2.50e+03 pdb=" C6 U A 66 " 0.003 2.00e-02 2.50e+03 ... (remaining 346 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 664 2.78 - 3.31: 2896 3.31 - 3.84: 5702 3.84 - 4.37: 6603 4.37 - 4.90: 9373 Nonbonded interactions: 25238 Sorted by model distance: nonbonded pdb=" C5 U A 24 " pdb=" N2 G A 44 " model vdw 2.249 3.420 nonbonded pdb=" O2' AN6 A 101 " pdb=" O3' AN6 A 101 " model vdw 2.335 2.432 nonbonded pdb=" O2' A A 23 " pdb=" O5' U A 24 " model vdw 2.407 3.040 nonbonded pdb=" O2' G A 9 " pdb=" OG SER B 114 " model vdw 2.411 3.040 nonbonded pdb=" C3' C A 64 " pdb=" OP2 U A 65 " model vdw 2.448 2.776 ... (remaining 25233 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.310 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.016 0.585 3299 Z= 1.324 Angle : 1.623 50.463 4801 Z= 1.028 Chirality : 0.114 2.398 591 Planarity : 0.004 0.026 349 Dihedral : 23.177 179.754 1742 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.31 % Allowed : 15.61 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 28.57 % 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: 0.59 (0.69), residues: 186 helix: 1.76 (0.70), residues: 64 sheet: 0.08 (1.24), residues: 23 loop : -0.41 (0.72), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 147 TYR 0.007 0.001 TYR B 237 PHE 0.004 0.001 PHE B 132 TRP 0.004 0.001 TRP B 160 HIS 0.001 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.01594 / 1.32 ( 3298) covalent geometry : angle 1.62271 / 1.03 ( 4801) hydrogen bonds : bond 0.14973 / 17.62 ( 97) hydrogen bonds : angle 9.03518 / 10.40 ( 221) Misc. bond : bond 0.01897 / 0.95 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: B 98 ILE cc_start: 0.9020 (mm) cc_final: 0.8323 (mm) REVERT: B 115 LEU cc_start: 0.9823 (tp) cc_final: 0.9588 (tt) REVERT: B 140 PHE cc_start: 0.7493 (m-80) cc_final: 0.6910 (m-80) REVERT: B 191 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8674 (mm-30) REVERT: B 213 ARG cc_start: 0.9551 (ttm170) cc_final: 0.9141 (ttp-110) REVERT: B 225 MET cc_start: 0.8579 (mmm) cc_final: 0.7745 (mmm) REVERT: B 253 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7994 (tm-30) REVERT: B 254 LEU cc_start: 0.9491 (mt) cc_final: 0.9254 (mt) outliers start: 4 outliers final: 0 residues processed: 37 average time/residue: 0.1051 time to fit residues: 4.4579 Evaluate side-chains 24 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.080112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.066734 restraints weight = 21797.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.068660 restraints weight = 12266.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.069730 restraints weight = 8801.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.070615 restraints weight = 7222.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.070791 restraints weight = 6240.328| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3299 Z= 0.167 Angle : 1.225 44.104 4801 Z= 0.500 Chirality : 0.042 0.346 591 Planarity : 0.005 0.037 349 Dihedral : 23.522 177.093 1337 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.16 % Allowed : 20.23 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 28.57 % 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: 0.09 (0.65), residues: 186 helix: 1.25 (0.61), residues: 64 sheet: -1.43 (1.10), residues: 28 loop : -0.19 (0.71), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 147 TYR 0.016 0.002 TYR B 185 PHE 0.011 0.002 PHE B 103 TRP 0.004 0.001 TRP B 264 HIS 0.010 0.002 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.17 ( 3298) covalent geometry : angle 1.22491 / 0.50 ( 4801) hydrogen bonds : bond 0.06191 / 6.64 ( 97) hydrogen bonds : angle 6.82230 / 7.53 ( 221) Misc. bond : bond 0.01227 / 0.61 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: B 109 ASP cc_start: 0.9039 (m-30) cc_final: 0.8757 (p0) REVERT: B 140 PHE cc_start: 0.7461 (m-80) cc_final: 0.6974 (m-10) REVERT: B 191 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8625 (mm-30) REVERT: B 201 MET cc_start: 0.8034 (mmm) cc_final: 0.7793 (mmm) REVERT: B 213 ARG cc_start: 0.9541 (ttm170) cc_final: 0.9180 (ttp-110) REVERT: B 225 MET cc_start: 0.8230 (mmm) cc_final: 0.7922 (mmm) REVERT: B 253 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8026 (tm-30) outliers start: 2 outliers final: 1 residues processed: 31 average time/residue: 0.0620 time to fit residues: 2.3529 Evaluate side-chains 24 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.079782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.066218 restraints weight = 21434.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.068207 restraints weight = 11730.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.069283 restraints weight = 8242.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.070089 restraints weight = 6761.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.070569 restraints weight = 5877.261| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3299 Z= 0.143 Angle : 0.592 10.146 4801 Z= 0.334 Chirality : 0.036 0.174 591 Planarity : 0.005 0.033 349 Dihedral : 23.316 178.892 1337 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.89 % Allowed : 21.97 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 28.57 % 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: 0.04 (0.63), residues: 186 helix: 1.13 (0.61), residues: 64 sheet: -1.26 (1.13), residues: 28 loop : -0.24 (0.68), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 143 TYR 0.005 0.001 TYR B 237 PHE 0.007 0.001 PHE B 259 TRP 0.003 0.001 TRP B 264 HIS 0.006 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 ( 3298) covalent geometry : angle 0.59214 / 0.33 ( 4801) hydrogen bonds : bond 0.06265 / 6.54 ( 97) hydrogen bonds : angle 6.36154 / 7.23 ( 221) Misc. bond : bond 0.00274 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: B 109 ASP cc_start: 0.9038 (m-30) cc_final: 0.8790 (p0) REVERT: B 140 PHE cc_start: 0.7646 (m-80) cc_final: 0.7028 (m-10) REVERT: B 191 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8550 (mm-30) REVERT: B 201 MET cc_start: 0.8074 (mmm) cc_final: 0.7871 (mmm) REVERT: B 213 ARG cc_start: 0.9553 (ttm170) cc_final: 0.9191 (ttp-110) REVERT: B 225 MET cc_start: 0.8366 (mmm) cc_final: 0.8012 (mmm) REVERT: B 253 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8021 (tm-30) outliers start: 5 outliers final: 3 residues processed: 30 average time/residue: 0.0604 time to fit residues: 2.2917 Evaluate side-chains 25 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 218 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 117 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 = 0.3764 r_free = 0.3764 target = 0.078057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.064830 restraints weight = 21158.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.066678 restraints weight = 11595.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.067704 restraints weight = 8240.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.068512 restraints weight = 6787.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.068933 restraints weight = 5892.041| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3299 Z= 0.124 Angle : 0.504 5.716 4801 Z= 0.291 Chirality : 0.033 0.131 591 Planarity : 0.004 0.030 349 Dihedral : 23.302 176.630 1337 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.62 % Allowed : 19.65 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 28.57 % 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: 0.06 (0.63), residues: 186 helix: 1.03 (0.64), residues: 64 sheet: -0.85 (1.02), residues: 33 loop : -0.23 (0.68), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 147 TYR 0.005 0.001 TYR B 237 PHE 0.007 0.001 PHE B 259 TRP 0.003 0.001 TRP B 264 HIS 0.003 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 ( 3298) covalent geometry : angle 0.50382 / 0.29 ( 4801) hydrogen bonds : bond 0.06316 / 6.48 ( 97) hydrogen bonds : angle 5.95185 / 6.87 ( 221) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.105 Fit side-chains REVERT: B 109 ASP cc_start: 0.9077 (m-30) cc_final: 0.8792 (p0) REVERT: B 140 PHE cc_start: 0.7680 (m-80) cc_final: 0.7056 (m-10) REVERT: B 191 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8576 (mm-30) REVERT: B 213 ARG cc_start: 0.9541 (ttm170) cc_final: 0.9181 (ttp-110) REVERT: B 225 MET cc_start: 0.8431 (mmm) cc_final: 0.8099 (mmm) REVERT: B 253 GLN cc_start: 0.8462 (tm-30) cc_final: 0.7981 (tm-30) outliers start: 8 outliers final: 4 residues processed: 28 average time/residue: 0.0628 time to fit residues: 2.2458 Evaluate side-chains 26 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 246 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 18 optimal weight: 0.0010 chunk 4 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.075260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.061713 restraints weight = 21732.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.063597 restraints weight = 11983.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.064713 restraints weight = 8596.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.065286 restraints weight = 6991.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.065482 restraints weight = 6246.047| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3299 Z= 0.171 Angle : 0.622 11.866 4801 Z= 0.337 Chirality : 0.035 0.132 591 Planarity : 0.005 0.033 349 Dihedral : 23.498 179.652 1337 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.05 % Allowed : 20.81 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 28.57 % 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: -0.01 (0.64), residues: 186 helix: 0.81 (0.63), residues: 64 sheet: -1.04 (1.00), residues: 34 loop : -0.03 (0.71), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 202 TYR 0.010 0.002 TYR B 123 PHE 0.017 0.002 PHE B 259 TRP 0.003 0.001 TRP B 264 HIS 0.002 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 ( 3298) covalent geometry : angle 0.62193 / 0.34 ( 4801) hydrogen bonds : bond 0.07125 / 7.34 ( 97) hydrogen bonds : angle 5.83999 / 6.85 ( 221) Misc. bond : bond 0.00068 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.102 Fit side-chains REVERT: B 107 MET cc_start: 0.7497 (mmt) cc_final: 0.7218 (mmm) REVERT: B 109 ASP cc_start: 0.9133 (m-30) cc_final: 0.8787 (p0) REVERT: B 140 PHE cc_start: 0.7685 (m-80) cc_final: 0.7132 (m-10) REVERT: B 191 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8605 (mm-30) REVERT: B 201 MET cc_start: 0.8216 (mmm) cc_final: 0.7895 (mmm) REVERT: B 213 ARG cc_start: 0.9541 (ttm170) cc_final: 0.9200 (ttp-110) REVERT: B 225 MET cc_start: 0.8459 (mmm) cc_final: 0.8117 (mmm) REVERT: B 253 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7960 (tm-30) outliers start: 7 outliers final: 4 residues processed: 28 average time/residue: 0.0628 time to fit residues: 2.2064 Evaluate side-chains 26 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 218 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** 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 = 0.3691 r_free = 0.3691 target = 0.074353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.060648 restraints weight = 21935.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.062521 restraints weight = 12069.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.063524 restraints weight = 8636.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.064271 restraints weight = 7163.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.064485 restraints weight = 6260.994| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3299 Z= 0.138 Angle : 0.503 4.532 4801 Z= 0.291 Chirality : 0.034 0.169 591 Planarity : 0.004 0.028 349 Dihedral : 23.564 179.759 1337 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.05 % Allowed : 20.81 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 28.57 % 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: 0.11 (0.65), residues: 186 helix: 0.86 (0.63), residues: 64 sheet: -0.87 (1.02), residues: 34 loop : 0.03 (0.72), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 230 TYR 0.008 0.001 TYR B 185 PHE 0.012 0.002 PHE B 259 TRP 0.003 0.001 TRP B 264 HIS 0.001 0.001 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 3298) covalent geometry : angle 0.50331 / 0.29 ( 4801) hydrogen bonds : bond 0.06526 / 6.73 ( 97) hydrogen bonds : angle 5.83133 / 6.79 ( 221) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: B 109 ASP cc_start: 0.9209 (m-30) cc_final: 0.8886 (p0) REVERT: B 140 PHE cc_start: 0.7885 (m-80) cc_final: 0.7275 (m-10) REVERT: B 191 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8697 (mm-30) REVERT: B 201 MET cc_start: 0.8177 (mmm) cc_final: 0.7765 (mmm) REVERT: B 213 ARG cc_start: 0.9538 (ttm170) cc_final: 0.9172 (ttp-110) REVERT: B 225 MET cc_start: 0.8488 (mmm) cc_final: 0.8142 (mmm) outliers start: 7 outliers final: 4 residues processed: 27 average time/residue: 0.0490 time to fit residues: 1.7042 Evaluate side-chains 26 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 218 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 0.3980 chunk 1 optimal weight: 20.0000 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.073933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.060460 restraints weight = 22180.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.062385 restraints weight = 11762.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.063507 restraints weight = 8212.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.064019 restraints weight = 6689.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.064553 restraints weight = 6004.677| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 3299 Z= 0.117 Angle : 0.545 8.423 4801 Z= 0.306 Chirality : 0.034 0.155 591 Planarity : 0.004 0.026 349 Dihedral : 23.485 179.904 1337 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.89 % Allowed : 24.28 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 28.57 % 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: 0.15 (0.65), residues: 186 helix: 0.86 (0.64), residues: 63 sheet: -0.95 (1.01), residues: 34 loop : 0.16 (0.72), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 143 TYR 0.008 0.002 TYR B 214 PHE 0.007 0.001 PHE B 259 TRP 0.004 0.001 TRP B 160 HIS 0.003 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 3298) covalent geometry : angle 0.54486 / 0.31 ( 4801) hydrogen bonds : bond 0.06155 / 6.30 ( 97) hydrogen bonds : angle 5.70432 / 6.62 ( 221) Misc. bond : bond 0.00050 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.084 Fit side-chains REVERT: B 109 ASP cc_start: 0.9136 (m-30) cc_final: 0.8838 (p0) REVERT: B 140 PHE cc_start: 0.7812 (m-80) cc_final: 0.7233 (m-10) REVERT: B 191 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8632 (mm-30) REVERT: B 201 MET cc_start: 0.8256 (mmm) cc_final: 0.7901 (mmm) REVERT: B 225 MET cc_start: 0.8460 (mmm) cc_final: 0.8088 (mmm) REVERT: B 253 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8122 (tm-30) outliers start: 5 outliers final: 3 residues processed: 24 average time/residue: 0.0432 time to fit residues: 1.4771 Evaluate side-chains 24 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 218 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 15 optimal weight: 0.0870 chunk 6 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.072975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.059590 restraints weight = 22515.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.061437 restraints weight = 11999.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.062574 restraints weight = 8445.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.063268 restraints weight = 6824.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.063614 restraints weight = 5973.400| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3299 Z= 0.122 Angle : 0.533 8.177 4801 Z= 0.305 Chirality : 0.035 0.169 591 Planarity : 0.004 0.026 349 Dihedral : 23.450 179.480 1337 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.31 % Allowed : 25.43 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 28.57 % 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: 0.08 (0.65), residues: 186 helix: 0.62 (0.62), residues: 63 sheet: -0.75 (1.01), residues: 34 loop : 0.16 (0.74), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 147 TYR 0.006 0.001 TYR B 237 PHE 0.009 0.001 PHE B 259 TRP 0.003 0.001 TRP B 160 HIS 0.002 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 ( 3298) covalent geometry : angle 0.53330 / 0.31 ( 4801) hydrogen bonds : bond 0.06288 / 6.35 ( 97) hydrogen bonds : angle 5.64330 / 6.50 ( 221) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.080 Fit side-chains REVERT: B 109 ASP cc_start: 0.9119 (m-30) cc_final: 0.8846 (p0) REVERT: B 140 PHE cc_start: 0.7772 (m-80) cc_final: 0.7201 (m-10) REVERT: B 201 MET cc_start: 0.8275 (mmm) cc_final: 0.7910 (mmm) REVERT: B 225 MET cc_start: 0.8550 (mmm) cc_final: 0.8184 (mmm) REVERT: B 253 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8125 (tm-30) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.0528 time to fit residues: 1.6295 Evaluate side-chains 24 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 218 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 5 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.072139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.058860 restraints weight = 22170.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.060704 restraints weight = 12149.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.061793 restraints weight = 8580.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.062489 restraints weight = 6975.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.062722 restraints weight = 6098.630| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3299 Z= 0.142 Angle : 0.559 7.976 4801 Z= 0.322 Chirality : 0.035 0.143 591 Planarity : 0.004 0.025 349 Dihedral : 23.539 178.649 1337 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.89 % Allowed : 24.28 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 28.57 % 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: 0.02 (0.64), residues: 186 helix: 0.63 (0.61), residues: 61 sheet: -0.76 (0.99), residues: 34 loop : 0.06 (0.72), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 213 TYR 0.007 0.001 TYR B 237 PHE 0.011 0.001 PHE B 259 TRP 0.003 0.001 TRP B 160 HIS 0.002 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 3298) covalent geometry : angle 0.55932 / 0.32 ( 4801) hydrogen bonds : bond 0.06740 / 6.83 ( 97) hydrogen bonds : angle 5.76794 / 6.60 ( 221) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.079 Fit side-chains REVERT: B 107 MET cc_start: 0.7994 (mmm) cc_final: 0.7737 (mmm) REVERT: B 109 ASP cc_start: 0.9204 (m-30) cc_final: 0.8897 (p0) REVERT: B 140 PHE cc_start: 0.7972 (m-80) cc_final: 0.7406 (m-10) REVERT: B 225 MET cc_start: 0.8507 (mmm) cc_final: 0.8142 (mmm) REVERT: B 253 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8275 (tm-30) outliers start: 5 outliers final: 4 residues processed: 24 average time/residue: 0.0665 time to fit residues: 2.0216 Evaluate side-chains 24 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 218 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.073183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.060069 restraints weight = 21718.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.061915 restraints weight = 11568.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.063032 restraints weight = 8069.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.063650 restraints weight = 6491.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.064124 restraints weight = 5755.290| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3299 Z= 0.110 Angle : 0.572 8.810 4801 Z= 0.326 Chirality : 0.035 0.172 591 Planarity : 0.004 0.023 349 Dihedral : 23.534 179.526 1337 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.73 % Allowed : 26.59 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 28.57 % 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: 0.09 (0.65), residues: 186 helix: 0.50 (0.63), residues: 61 sheet: -0.56 (0.96), residues: 34 loop : 0.19 (0.75), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 143 TYR 0.006 0.001 TYR B 237 PHE 0.006 0.001 PHE B 173 TRP 0.007 0.001 TRP B 160 HIS 0.002 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.11 ( 3298) covalent geometry : angle 0.57240 / 0.33 ( 4801) hydrogen bonds : bond 0.06035 / 6.11 ( 97) hydrogen bonds : angle 5.86968 / 6.66 ( 221) Misc. bond : bond 0.00050 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.081 Fit side-chains REVERT: B 107 MET cc_start: 0.7929 (mmm) cc_final: 0.7641 (mmm) REVERT: B 109 ASP cc_start: 0.9197 (m-30) cc_final: 0.8899 (p0) REVERT: B 140 PHE cc_start: 0.7934 (m-80) cc_final: 0.7343 (m-10) REVERT: B 191 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8626 (mm-30) REVERT: B 201 MET cc_start: 0.8112 (mmm) cc_final: 0.7268 (tpt) REVERT: B 225 MET cc_start: 0.8522 (mmm) cc_final: 0.8153 (mmm) REVERT: B 253 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8287 (tm-30) outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.0597 time to fit residues: 1.7926 Evaluate side-chains 25 residues out of total 173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 218 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 14 optimal weight: 0.0070 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.072716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.059629 restraints weight = 21894.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.061522 restraints weight = 11925.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.062504 restraints weight = 8365.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.063265 restraints weight = 6850.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.063493 restraints weight = 5937.271| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 3299 Z= 0.123 Angle : 0.575 11.362 4801 Z= 0.331 Chirality : 0.036 0.224 591 Planarity : 0.004 0.023 349 Dihedral : 23.546 179.823 1337 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.73 % Allowed : 26.01 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 28.57 % 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: -0.00 (0.65), residues: 186 helix: 0.25 (0.63), residues: 63 sheet: -0.45 (0.96), residues: 34 loop : 0.19 (0.76), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 121 TYR 0.006 0.001 TYR B 237 PHE 0.007 0.001 PHE B 259 TRP 0.004 0.001 TRP B 160 HIS 0.003 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 3298) covalent geometry : angle 0.57456 / 0.33 ( 4801) hydrogen bonds : bond 0.06335 / 6.30 ( 97) hydrogen bonds : angle 5.94450 / 6.65 ( 221) Misc. bond : bond 0.00024 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 831.39 seconds wall clock time: 14 minutes 58.22 seconds (898.22 seconds total)