Starting phenix.real_space_refine on Fri Sep 11 00:57:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhy_24471/09_2026/7rhy_24471_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhy_24471/09_2026/7rhy_24471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rhy_24471/09_2026/7rhy_24471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhy_24471/09_2026/7rhy_24471.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhy_24471/09_2026/7rhy_24471_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhy_24471/09_2026/7rhy_24471_neut.cif" } resolution = 3.91 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= 0.001 sd= 0.055 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: 6 Type Number sf(0) Gaussians P 49 5.49 5 S 14 5.16 5 C 1968 2.51 5 N 640 2.21 5 O 722 1.98 5 H 2957 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6350 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 4789 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 1 Chain: "B" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1561 Classifications: {'DNA': 49} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 48} Time building chain proxies: 1.32, per 1000 atoms: 0.21 Number of scatterers: 6350 At special positions: 0 Unit cell: (59.5055, 74.8617, 92.1375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 49 15.00 O 722 8.00 N 640 7.00 C 1968 6.00 H 2957 1.00 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=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 317.9 milliseconds 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 562 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 1 sheets defined 67.4% alpha, 3.3% beta 23 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 removed outlier: 3.665A pdb=" N MET A 30 " --> pdb=" O ASN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 59 removed outlier: 3.595A pdb=" N MET A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 46 " --> pdb=" O TRP A 42 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 47 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.507A pdb=" N ILE A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 109 Processing helix chain 'A' and resid 110 through 127 Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.651A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 170 removed outlier: 3.553A pdb=" N ASN A 160 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 179 through 180 No H-bonds generated for 'chain 'A' and resid 179 through 180' Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.916A pdb=" N LEU A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 233 removed outlier: 4.100A pdb=" N ASP A 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'A' and resid 257 through 273 removed outlier: 3.633A pdb=" N GLY A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.174A pdb=" N ALA A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 319 through 325 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 187 removed outlier: 4.177A pdb=" N MET A 193 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 209 " --> pdb=" O ILE A 197 " (cutoff:3.500A) 129 hydrogen bonds defined for protein. 384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2953 1.03 - 1.23: 29 1.23 - 1.42: 1533 1.42 - 1.61: 1974 1.61 - 1.81: 24 Bond restraints: 6513 Sorted by residual: bond pdb=" C3' DG B 46 " pdb=" C2' DG B 46 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.44e+01 bond pdb=" C3' DA B 44 " pdb=" C2' DA B 44 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.34e+01 bond pdb=" C3' DG B 9 " pdb=" C2' DG B 9 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C3' DG B 14 " pdb=" C2' DG B 14 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DT B 42 " pdb=" C2' DT B 42 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 ... (remaining 6508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 10739 1.36 - 2.72: 893 2.72 - 4.08: 77 4.08 - 5.44: 32 5.44 - 6.80: 5 Bond angle restraints: 11746 Sorted by residual: angle pdb=" O5' DT B 19 " pdb=" C5' DT B 19 " pdb=" C4' DT B 19 " ideal model delta sigma weight residual 109.40 113.93 -4.53 8.00e-01 1.56e+00 3.21e+01 angle pdb=" O4' DG B 22 " pdb=" C1' DG B 22 " pdb=" N9 DG B 22 " ideal model delta sigma weight residual 108.00 111.79 -3.79 7.00e-01 2.04e+00 2.93e+01 angle pdb=" C3' DC B 15 " pdb=" O3' DC B 15 " pdb=" P DA B 16 " ideal model delta sigma weight residual 119.70 125.87 -6.17 1.20e+00 6.94e-01 2.64e+01 angle pdb=" O5' DT B 35 " pdb=" C5' DT B 35 " pdb=" C4' DT B 35 " ideal model delta sigma weight residual 109.40 113.35 -3.95 8.00e-01 1.56e+00 2.44e+01 angle pdb=" O5' DG B 20 " pdb=" C5' DG B 20 " pdb=" C4' DG B 20 " ideal model delta sigma weight residual 109.40 113.32 -3.92 8.00e-01 1.56e+00 2.40e+01 ... (remaining 11741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.52: 2584 34.52 - 69.04: 281 69.04 - 103.57: 2 103.57 - 138.09: 0 138.09 - 172.61: 1 Dihedral angle restraints: 2868 sinusoidal: 1872 harmonic: 996 Sorted by residual: dihedral pdb=" CA ALA A 212 " pdb=" C ALA A 212 " pdb=" N LEU A 213 " pdb=" CA LEU A 213 " ideal model delta harmonic sigma weight residual -180.00 -154.53 -25.47 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA LYS A 211 " pdb=" C LYS A 211 " pdb=" N ALA A 212 " pdb=" CA ALA A 212 " ideal model delta harmonic sigma weight residual -180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO A 250 " pdb=" C PRO A 250 " pdb=" N SER A 251 " pdb=" CA SER A 251 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 2865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 411 0.052 - 0.104: 92 0.104 - 0.156: 33 0.156 - 0.208: 17 0.208 - 0.260: 1 Chirality restraints: 554 Sorted by residual: chirality pdb=" C3' DC B 15 " pdb=" C4' DC B 15 " pdb=" O3' DC B 15 " pdb=" C2' DC B 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C3' DT B 35 " pdb=" C4' DT B 35 " pdb=" O3' DT B 35 " pdb=" C2' DT B 35 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" C3' DA B 27 " pdb=" C4' DA B 27 " pdb=" O3' DA B 27 " pdb=" C2' DA B 27 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 551 not shown) Planarity restraints: 801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT B 10 " 0.041 2.00e-02 2.50e+03 4.29e-02 5.53e+01 pdb=" N1 DT B 10 " -0.119 2.00e-02 2.50e+03 pdb=" C2 DT B 10 " 0.076 2.00e-02 2.50e+03 pdb=" O2 DT B 10 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT B 10 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DT B 10 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT B 10 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DT B 10 " 0.004 2.00e-02 2.50e+03 pdb=" C7 DT B 10 " 0.009 2.00e-02 2.50e+03 pdb=" C6 DT B 10 " -0.001 2.00e-02 2.50e+03 pdb=" H3 DT B 10 " -0.009 2.00e-02 2.50e+03 pdb=" H6 DT B 10 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA B 11 " 0.039 2.00e-02 2.50e+03 2.98e-02 2.88e+01 pdb=" N9 DA B 11 " -0.088 2.00e-02 2.50e+03 pdb=" C8 DA B 11 " 0.046 2.00e-02 2.50e+03 pdb=" N7 DA B 11 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA B 11 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA B 11 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA B 11 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA B 11 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA B 11 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA B 11 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA B 11 " -0.004 2.00e-02 2.50e+03 pdb=" H8 DA B 11 " -0.005 2.00e-02 2.50e+03 pdb=" H2 DA B 11 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT B 7 " 0.028 2.00e-02 2.50e+03 2.56e-02 1.97e+01 pdb=" N1 DT B 7 " -0.073 2.00e-02 2.50e+03 pdb=" C2 DT B 7 " 0.041 2.00e-02 2.50e+03 pdb=" O2 DT B 7 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT B 7 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT B 7 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT B 7 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DT B 7 " 0.004 2.00e-02 2.50e+03 pdb=" C7 DT B 7 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT B 7 " 0.003 2.00e-02 2.50e+03 pdb=" H3 DT B 7 " -0.004 2.00e-02 2.50e+03 pdb=" H6 DT B 7 " 0.004 2.00e-02 2.50e+03 ... (remaining 798 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 219 2.19 - 2.80: 11394 2.80 - 3.40: 15364 3.40 - 4.00: 19680 4.00 - 4.60: 30595 Nonbonded interactions: 77252 Sorted by model distance: nonbonded pdb=" H ARG A 181 " pdb=" OD2 ASP A 184 " model vdw 1.593 2.450 nonbonded pdb=" HG1 THR A 41 " pdb=" OP2 DT B 33 " model vdw 1.605 2.450 nonbonded pdb="HH21 ARG A 297 " pdb=" O ASN A 327 " model vdw 1.732 2.450 nonbonded pdb="HH12 ARG A 61 " pdb=" OD1 ASP A 70 " model vdw 1.744 2.450 nonbonded pdb=" HG SER A 287 " pdb=" OP1 DA B 36 " model vdw 1.752 2.450 ... (remaining 77247 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: 1.030 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: 0.030 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.740 Find NCS groups from input model: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 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 : 0.006 0.035 3556 Z= 0.506 Angle : 0.911 6.800 5012 Z= 0.735 Chirality : 0.058 0.260 554 Planarity : 0.011 0.100 474 Dihedral : 21.980 172.609 1463 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.80 % Allowed : 1.60 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.45), residues: 297 helix: -1.09 (0.33), residues: 183 sheet: 2.44 (1.61), residues: 10 loop : 0.10 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG A 61 TYR 0.010 0.004 TYR A 237 PHE 0.009 0.003 PHE A 64 TRP 0.007 0.002 TRP A 55 HIS 0.005 0.002 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.51 ( 3556) covalent geometry : angle 0.91109 / 0.74 ( 5012) hydrogen bonds : bond 0.14353 / 9.20 ( 184) hydrogen bonds : angle 6.36246 / 4.74 ( 490) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 THR cc_start: 0.9297 (m) cc_final: 0.8996 (p) REVERT: A 308 GLU cc_start: 0.8446 (tt0) cc_final: 0.8064 (tm-30) REVERT: A 309 ILE cc_start: 0.8785 (mt) cc_final: 0.8556 (mt) outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 0.2356 time to fit residues: 21.1768 Evaluate side-chains 39 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.136199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103586 restraints weight = 17600.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109547 restraints weight = 8483.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.113607 restraints weight = 5383.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.116289 restraints weight = 3937.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118239 restraints weight = 3152.233| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3556 Z= 0.210 Angle : 0.712 6.450 5012 Z= 0.437 Chirality : 0.044 0.240 554 Planarity : 0.005 0.036 474 Dihedral : 25.678 175.477 889 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.80 % Allowed : 10.40 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.48), residues: 297 helix: -0.02 (0.37), residues: 187 sheet: 1.48 (1.46), residues: 10 loop : 0.02 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 154 TYR 0.015 0.002 TYR A 77 PHE 0.016 0.002 PHE A 163 TRP 0.004 0.001 TRP A 42 HIS 0.003 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.21 ( 3556) covalent geometry : angle 0.71245 / 0.44 ( 5012) hydrogen bonds : bond 0.07674 / 5.50 ( 184) hydrogen bonds : angle 5.33980 / 4.00 ( 490) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 THR cc_start: 0.9320 (m) cc_final: 0.9063 (p) outliers start: 7 outliers final: 7 residues processed: 48 average time/residue: 0.1203 time to fit residues: 7.1278 Evaluate side-chains 42 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.136157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.103843 restraints weight = 17451.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109936 restraints weight = 8253.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.113999 restraints weight = 5172.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.116816 restraints weight = 3765.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118799 restraints weight = 2967.487| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3556 Z= 0.175 Angle : 0.631 6.583 5012 Z= 0.395 Chirality : 0.041 0.244 554 Planarity : 0.004 0.032 474 Dihedral : 25.721 174.977 889 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.60 % Allowed : 15.20 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.48), residues: 297 helix: 0.47 (0.38), residues: 186 sheet: 1.10 (1.58), residues: 10 loop : 0.10 (0.62), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 154 TYR 0.014 0.001 TYR A 77 PHE 0.012 0.002 PHE A 37 TRP 0.007 0.001 TRP A 42 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 ( 3556) covalent geometry : angle 0.63075 / 0.40 ( 5012) hydrogen bonds : bond 0.06904 / 5.05 ( 184) hydrogen bonds : angle 4.93387 / 3.67 ( 490) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.8123 (mt0) cc_final: 0.7783 (mt0) REVERT: A 170 THR cc_start: 0.9301 (m) cc_final: 0.9079 (p) REVERT: A 316 THR cc_start: 0.8548 (m) cc_final: 0.8255 (p) outliers start: 4 outliers final: 4 residues processed: 41 average time/residue: 0.0686 time to fit residues: 4.1635 Evaluate side-chains 37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 166 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.135639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102751 restraints weight = 17556.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.108806 restraints weight = 8386.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112850 restraints weight = 5331.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.115680 restraints weight = 3911.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117600 restraints weight = 3102.355| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3556 Z= 0.180 Angle : 0.625 6.740 5012 Z= 0.388 Chirality : 0.040 0.251 554 Planarity : 0.004 0.032 474 Dihedral : 25.754 175.104 889 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.00 % Allowed : 16.00 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.49), residues: 297 helix: 0.79 (0.39), residues: 186 sheet: 0.77 (1.59), residues: 10 loop : 0.05 (0.62), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.011 0.001 TYR A 77 PHE 0.011 0.002 PHE A 163 TRP 0.006 0.001 TRP A 42 HIS 0.003 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.18 ( 3556) covalent geometry : angle 0.62518 / 0.39 ( 5012) hydrogen bonds : bond 0.06514 / 4.73 ( 184) hydrogen bonds : angle 4.80477 / 3.58 ( 490) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.8057 (mt0) cc_final: 0.7824 (mt0) REVERT: A 176 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7295 (mt-10) REVERT: A 316 THR cc_start: 0.8597 (m) cc_final: 0.8315 (p) REVERT: A 323 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7906 (t0) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.0668 time to fit residues: 3.8272 Evaluate side-chains 39 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 323 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.136652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104084 restraints weight = 17527.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.110258 restraints weight = 8268.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.114398 restraints weight = 5183.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.117233 restraints weight = 3758.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.118964 restraints weight = 2972.363| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3556 Z= 0.152 Angle : 0.586 6.396 5012 Z= 0.370 Chirality : 0.039 0.248 554 Planarity : 0.004 0.034 474 Dihedral : 25.741 174.108 889 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.60 % Allowed : 16.40 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.50), residues: 297 helix: 1.06 (0.40), residues: 186 sheet: 0.89 (1.58), residues: 10 loop : 0.07 (0.63), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 101 TYR 0.010 0.001 TYR A 77 PHE 0.011 0.002 PHE A 37 TRP 0.006 0.001 TRP A 42 HIS 0.003 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.15 ( 3556) covalent geometry : angle 0.58583 / 0.37 ( 5012) hydrogen bonds : bond 0.05953 / 4.35 ( 184) hydrogen bonds : angle 4.57667 / 3.40 ( 490) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7302 (mt-10) REVERT: A 316 THR cc_start: 0.8591 (m) cc_final: 0.8336 (p) outliers start: 4 outliers final: 4 residues processed: 38 average time/residue: 0.0696 time to fit residues: 3.9955 Evaluate side-chains 37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 166 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.136207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103563 restraints weight = 17451.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.109633 restraints weight = 8215.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.113836 restraints weight = 5178.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.116638 restraints weight = 3744.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.118516 restraints weight = 2972.677| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3556 Z= 0.156 Angle : 0.597 6.980 5012 Z= 0.371 Chirality : 0.039 0.254 554 Planarity : 0.003 0.033 474 Dihedral : 25.730 173.733 889 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.60 % Allowed : 16.80 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.51), residues: 297 helix: 1.30 (0.41), residues: 187 sheet: 0.53 (1.38), residues: 10 loop : -0.03 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.010 0.001 TYR A 77 PHE 0.009 0.002 PHE A 163 TRP 0.004 0.000 TRP A 42 HIS 0.003 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.16 ( 3556) covalent geometry : angle 0.59740 / 0.37 ( 5012) hydrogen bonds : bond 0.05783 / 4.26 ( 184) hydrogen bonds : angle 4.42032 / 3.26 ( 490) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7316 (mt-10) REVERT: A 316 THR cc_start: 0.8566 (m) cc_final: 0.8299 (p) outliers start: 4 outliers final: 4 residues processed: 36 average time/residue: 0.0580 time to fit residues: 3.1224 Evaluate side-chains 38 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 166 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.136477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103777 restraints weight = 17574.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109924 restraints weight = 8259.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.114080 restraints weight = 5201.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.116785 restraints weight = 3782.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118726 restraints weight = 3024.344| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3556 Z= 0.146 Angle : 0.575 7.284 5012 Z= 0.361 Chirality : 0.039 0.252 554 Planarity : 0.003 0.033 474 Dihedral : 25.726 173.246 889 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.00 % Allowed : 16.00 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.50), residues: 297 helix: 1.40 (0.40), residues: 187 sheet: 0.44 (1.31), residues: 10 loop : -0.13 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.009 0.001 TYR A 77 PHE 0.008 0.002 PHE A 265 TRP 0.005 0.000 TRP A 42 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.15 ( 3556) covalent geometry : angle 0.57514 / 0.36 ( 5012) hydrogen bonds : bond 0.05612 / 4.15 ( 184) hydrogen bonds : angle 4.34013 / 3.20 ( 490) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7235 (mt-10) REVERT: A 316 THR cc_start: 0.8554 (m) cc_final: 0.8298 (p) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.0644 time to fit residues: 3.6843 Evaluate side-chains 38 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 166 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.0000 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 23 optimal weight: 0.0980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.137048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.104368 restraints weight = 17549.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.110549 restraints weight = 8166.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.114728 restraints weight = 5108.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117563 restraints weight = 3699.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119490 restraints weight = 2924.386| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3556 Z= 0.140 Angle : 0.571 7.958 5012 Z= 0.358 Chirality : 0.039 0.252 554 Planarity : 0.003 0.034 474 Dihedral : 25.715 172.843 889 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.60 % Allowed : 17.20 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.50), residues: 297 helix: 1.53 (0.40), residues: 187 sheet: 0.56 (1.26), residues: 10 loop : -0.08 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.008 0.001 TYR A 77 PHE 0.007 0.001 PHE A 265 TRP 0.005 0.000 TRP A 42 HIS 0.002 0.000 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.14 ( 3556) covalent geometry : angle 0.57126 / 0.36 ( 5012) hydrogen bonds : bond 0.05349 / 3.99 ( 184) hydrogen bonds : angle 4.19983 / 3.10 ( 490) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 316 THR cc_start: 0.8543 (m) cc_final: 0.8298 (p) outliers start: 4 outliers final: 4 residues processed: 38 average time/residue: 0.0879 time to fit residues: 4.5456 Evaluate side-chains 35 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 166 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.136653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103939 restraints weight = 17846.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.110145 restraints weight = 8200.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.114332 restraints weight = 5118.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117082 restraints weight = 3686.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.118969 restraints weight = 2929.467| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3556 Z= 0.147 Angle : 0.577 8.270 5012 Z= 0.361 Chirality : 0.039 0.253 554 Planarity : 0.003 0.033 474 Dihedral : 25.716 172.612 889 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.60 % Allowed : 18.00 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.50), residues: 297 helix: 1.52 (0.40), residues: 187 sheet: 0.72 (1.25), residues: 10 loop : -0.16 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.008 0.001 TYR A 77 PHE 0.008 0.002 PHE A 163 TRP 0.004 0.000 TRP A 42 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.15 ( 3556) covalent geometry : angle 0.57694 / 0.36 ( 5012) hydrogen bonds : bond 0.05380 / 4.01 ( 184) hydrogen bonds : angle 4.22065 / 3.12 ( 490) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: A 316 THR cc_start: 0.8576 (m) cc_final: 0.8322 (p) outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.0596 time to fit residues: 2.8382 Evaluate side-chains 35 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.136028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103296 restraints weight = 17570.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109395 restraints weight = 8269.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.113498 restraints weight = 5218.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.116150 restraints weight = 3797.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117853 restraints weight = 3050.528| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3556 Z= 0.154 Angle : 0.585 8.648 5012 Z= 0.364 Chirality : 0.039 0.253 554 Planarity : 0.003 0.033 474 Dihedral : 25.715 172.396 889 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.60 % Allowed : 18.00 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.50), residues: 297 helix: 1.55 (0.40), residues: 187 sheet: 1.12 (1.32), residues: 10 loop : -0.36 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 101 TYR 0.010 0.001 TYR A 273 PHE 0.009 0.002 PHE A 163 TRP 0.004 0.001 TRP A 42 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 ( 3556) covalent geometry : angle 0.58519 / 0.36 ( 5012) hydrogen bonds : bond 0.05551 / 4.11 ( 184) hydrogen bonds : angle 4.25364 / 3.15 ( 490) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 316 THR cc_start: 0.8596 (m) cc_final: 0.8367 (p) outliers start: 4 outliers final: 4 residues processed: 35 average time/residue: 0.0702 time to fit residues: 3.6331 Evaluate side-chains 36 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.135395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103116 restraints weight = 17630.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109320 restraints weight = 8042.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.113320 restraints weight = 4964.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.115918 restraints weight = 3604.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.117765 restraints weight = 2890.994| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3556 Z= 0.165 Angle : 0.581 7.953 5012 Z= 0.364 Chirality : 0.039 0.253 554 Planarity : 0.003 0.033 474 Dihedral : 25.715 172.416 889 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.60 % Allowed : 18.00 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.50), residues: 297 helix: 1.57 (0.40), residues: 187 sheet: 1.10 (1.32), residues: 10 loop : -0.41 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 81 TYR 0.010 0.001 TYR A 273 PHE 0.009 0.002 PHE A 163 TRP 0.011 0.001 TRP A 42 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.17 ( 3556) covalent geometry : angle 0.58065 / 0.36 ( 5012) hydrogen bonds : bond 0.05673 / 4.16 ( 184) hydrogen bonds : angle 4.30528 / 3.20 ( 490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1426.87 seconds wall clock time: 24 minutes 55.66 seconds (1495.66 seconds total)