Starting phenix.real_space_refine on Fri Jul 3 04:38:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11ic_75710/07_2026/11ic_75710.cif Found real_map, /net/cci-nas-00/data/ceres_data/11ic_75710/07_2026/11ic_75710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11ic_75710/07_2026/11ic_75710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11ic_75710/07_2026/11ic_75710.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11ic_75710/07_2026/11ic_75710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11ic_75710/07_2026/11ic_75710.map" } resolution = 2.63 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= 0.013 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: 7 Type Number sf(0) Gaussians P 203 5.49 5 Mg 1 5.21 5 S 17 5.16 5 C 3610 2.51 5 N 1295 2.21 5 O 1875 1.98 5 H 4938 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11939 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5411 Classifications: {'peptide': 334} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 1 Chain: "B" Number of atoms: 6035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 6035 Classifications: {'RNA': 187} Modifications used: {'3*END': 1, 'rna2p_pur': 17, 'rna2p_pyr': 13, 'rna3p_pur': 93, 'rna3p_pyr': 64} Link IDs: {'rna2p': 29, 'rna3p': 157} Chain breaks: 1 Chain: "C" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 492 Classifications: {'RNA': 16} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 14} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.22, per 1000 atoms: 0.19 Number of scatterers: 11939 At special positions: 0 Unit cell: (88.275, 123.75, 123.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 17 16.00 P 203 15.00 Mg 1 11.99 O 1875 8.00 N 1295 7.00 C 3610 6.00 H 4938 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: 0.88 Conformation dependent library (CDL) restraints added in 151.4 milliseconds 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 634 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 4 sheets defined 37.4% alpha, 14.1% beta 72 base pairs and 126 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 88 through 108 removed outlier: 4.570A pdb=" N LYS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 163 through 184 removed outlier: 3.893A pdb=" N ILE A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 314 Proline residue: A 304 - end of helix removed outlier: 3.530A pdb=" N ASP A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 341 through 349 Processing helix chain 'A' and resid 408 through 415 Processing helix chain 'A' and resid 417 through 423 removed outlier: 3.714A pdb=" N LYS A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 5.280A pdb=" N MET A 15 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL A 6 " --> pdb=" O MET A 15 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TYR A 5 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU A 44 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE A 7 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 191 removed outlier: 6.493A pdb=" N LEU A 55 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL A 190 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 57 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE A 66 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN A 82 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N MET A 68 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASN A 80 " --> pdb=" O MET A 68 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 70 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A 82 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 367 " --> pdb=" O GLN A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA4, first strand: chain 'A' and resid 392 through 395 removed outlier: 6.922A pdb=" N TYR A 387 " --> pdb=" O VAL A 394 " (cutoff:3.500A) 101 hydrogen bonds defined for protein. 285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 183 hydrogen bonds 338 hydrogen bond angles 0 basepair planarities 72 basepair parallelities 126 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 4930 1.03 - 1.22: 51 1.22 - 1.42: 3395 1.42 - 1.61: 4099 1.61 - 1.81: 29 Bond restraints: 12504 Sorted by residual: bond pdb=" N9 A B 117 " pdb=" C4 A B 117 " ideal model delta sigma weight residual 1.374 1.362 0.012 6.00e-03 2.78e+04 4.18e+00 bond pdb=" N9 A B 189 " pdb=" C4 A B 189 " ideal model delta sigma weight residual 1.374 1.363 0.011 6.00e-03 2.78e+04 3.34e+00 bond pdb=" N3 A B 189 " pdb=" C4 A B 189 " ideal model delta sigma weight residual 1.344 1.333 0.011 6.00e-03 2.78e+04 3.19e+00 bond pdb=" O5' U C 11 " pdb=" C5' U C 11 " ideal model delta sigma weight residual 1.420 1.447 -0.027 1.50e-02 4.44e+03 3.13e+00 bond pdb=" O5' C C 8 " pdb=" C5' C C 8 " ideal model delta sigma weight residual 1.420 1.445 -0.025 1.50e-02 4.44e+03 2.83e+00 ... (remaining 12499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 21492 1.48 - 2.96: 837 2.96 - 4.44: 136 4.44 - 5.91: 12 5.91 - 7.39: 5 Bond angle restraints: 22482 Sorted by residual: angle pdb=" C1' U B 97 " pdb=" N1 U B 97 " pdb=" C2 U B 97 " ideal model delta sigma weight residual 117.70 123.88 -6.18 1.20e+00 6.94e-01 2.65e+01 angle pdb=" O3' A C 9 " pdb=" C3' A C 9 " pdb=" C2' A C 9 " ideal model delta sigma weight residual 113.70 120.26 -6.56 1.50e+00 4.44e-01 1.91e+01 angle pdb=" C4' A C 9 " pdb=" C3' A C 9 " pdb=" C2' A C 9 " ideal model delta sigma weight residual 102.60 98.23 4.37 1.00e+00 1.00e+00 1.91e+01 angle pdb=" N1 U B 97 " pdb=" C2 U B 97 " pdb=" O2 U B 97 " ideal model delta sigma weight residual 122.80 125.85 -3.05 7.00e-01 2.04e+00 1.90e+01 angle pdb=" O2 U B 97 " pdb=" C2 U B 97 " pdb=" N3 U B 97 " ideal model delta sigma weight residual 122.20 119.49 2.71 7.00e-01 2.04e+00 1.50e+01 ... (remaining 22477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.31: 5455 33.31 - 66.62: 570 66.62 - 99.93: 73 99.93 - 133.24: 3 133.24 - 166.55: 8 Dihedral angle restraints: 6109 sinusoidal: 4993 harmonic: 1116 Sorted by residual: dihedral pdb=" O4' C B 49 " pdb=" C1' C B 49 " pdb=" N1 C B 49 " pdb=" C2 C B 49 " ideal model delta sinusoidal sigma weight residual 200.00 34.02 165.98 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' C B 83 " pdb=" C1' C B 83 " pdb=" N1 C B 83 " pdb=" C2 C B 83 " ideal model delta sinusoidal sigma weight residual 232.00 65.45 166.55 1 1.70e+01 3.46e-03 6.55e+01 dihedral pdb=" O4' U B 96 " pdb=" C1' U B 96 " pdb=" N1 U B 96 " pdb=" C2 U B 96 " ideal model delta sinusoidal sigma weight residual -128.00 36.49 -164.49 1 1.70e+01 3.46e-03 6.52e+01 ... (remaining 6106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1380 0.094 - 0.188: 33 0.188 - 0.282: 1 0.282 - 0.376: 0 0.376 - 0.470: 4 Chirality restraints: 1418 Sorted by residual: chirality pdb=" P U C 11 " pdb=" OP1 U C 11 " pdb=" OP2 U C 11 " pdb=" O5' U C 11 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.53e+00 chirality pdb=" P C C 8 " pdb=" OP1 C C 8 " pdb=" OP2 C C 8 " pdb=" O5' C C 8 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" P C C 10 " pdb=" OP1 C C 10 " pdb=" OP2 C C 10 " pdb=" O5' C C 10 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.77e+00 ... (remaining 1415 not shown) Planarity restraints: 1147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 80 " 0.029 2.00e-02 2.50e+03 1.15e-02 4.61e+00 pdb=" N9 G B 80 " -0.029 2.00e-02 2.50e+03 pdb=" C8 G B 80 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G B 80 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B 80 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B 80 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 80 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G B 80 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G B 80 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 80 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 80 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G B 80 " -0.004 2.00e-02 2.50e+03 pdb=" H8 G B 80 " -0.000 2.00e-02 2.50e+03 pdb=" H1 G B 80 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 203 " 0.024 2.00e-02 2.50e+03 1.06e-02 3.66e+00 pdb=" N9 A B 203 " -0.029 2.00e-02 2.50e+03 pdb=" C8 A B 203 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A B 203 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A B 203 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B 203 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 203 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A B 203 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 203 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A B 203 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A B 203 " 0.001 2.00e-02 2.50e+03 pdb=" H8 A B 203 " 0.000 2.00e-02 2.50e+03 pdb=" H2 A B 203 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 56 " -0.025 2.00e-02 2.50e+03 1.06e-02 3.65e+00 pdb=" N9 A B 56 " 0.026 2.00e-02 2.50e+03 pdb=" C8 A B 56 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 56 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A B 56 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 56 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 56 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A B 56 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A B 56 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A B 56 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B 56 " 0.003 2.00e-02 2.50e+03 pdb=" H8 A B 56 " -0.001 2.00e-02 2.50e+03 pdb=" H2 A B 56 " 0.004 2.00e-02 2.50e+03 ... (remaining 1144 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.40: 4446 2.40 - 2.95: 22721 2.95 - 3.50: 30862 3.50 - 4.05: 44914 4.05 - 4.60: 60404 Nonbonded interactions: 163347 Sorted by model distance: nonbonded pdb="HO2' A B 86 " pdb=" H2' C B 87 " model vdw 1.852 2.270 nonbonded pdb=" H2' A B 2 " pdb=" H8 A B 3 " model vdw 1.865 2.270 nonbonded pdb=" HD1 PHE A 152 " pdb="HO2' U C 7 " model vdw 1.870 2.100 nonbonded pdb=" H2' G B 40 " pdb=" H8 A B 41 " model vdw 1.870 2.270 nonbonded pdb=" H VAL A 394 " pdb=" H ALA A 395 " model vdw 1.899 2.100 ... (remaining 163342 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.160 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: 0.060 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.910 Find NCS groups from input model: 0.030 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:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.004 0.037 7566 Z= 0.356 Angle : 0.597 7.392 11208 Z= 0.480 Chirality : 0.042 0.470 1418 Planarity : 0.004 0.036 673 Dihedral : 22.242 166.546 4166 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.50), residues: 330 helix: 2.06 (0.54), residues: 112 sheet: -1.98 (0.73), residues: 49 loop : -0.69 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 115 TYR 0.011 0.001 TYR A 5 PHE 0.008 0.001 PHE A 79 TRP 0.005 0.001 TRP A 161 HIS 0.002 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.36 ( 7566) covalent geometry : angle 0.59676 / 0.48 (11208) hydrogen bonds : bond 0.11078 / 7.43 ( 284) hydrogen bonds : angle 4.51414 / 3.31 ( 623) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8249 (ttp-170) REVERT: A 36 GLU cc_start: 0.7914 (tt0) cc_final: 0.7699 (tt0) REVERT: A 69 SER cc_start: 0.8968 (t) cc_final: 0.8482 (m) REVERT: A 179 LYS cc_start: 0.8214 (tppp) cc_final: 0.7714 (ttpt) REVERT: A 339 HIS cc_start: 0.6737 (t70) cc_final: 0.6365 (t-170) REVERT: A 342 ASP cc_start: 0.8515 (m-30) cc_final: 0.8189 (m-30) REVERT: A 386 SER cc_start: 0.8523 (m) cc_final: 0.8143 (p) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.9893 time to fit residues: 79.9994 Evaluate side-chains 50 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.115483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.072591 restraints weight = 28335.973| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.49 r_work: 0.2968 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7566 Z= 0.144 Angle : 0.470 5.205 11208 Z= 0.287 Chirality : 0.034 0.186 1418 Planarity : 0.004 0.034 673 Dihedral : 23.288 168.630 3482 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.69 % Allowed : 12.46 % Favored : 86.85 % 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: 0.22 (0.49), residues: 330 helix: 2.17 (0.53), residues: 113 sheet: -1.78 (0.73), residues: 49 loop : -0.62 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 146 TYR 0.011 0.001 TYR A 344 PHE 0.006 0.001 PHE A 79 TRP 0.004 0.001 TRP A 161 HIS 0.006 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 ( 7566) covalent geometry : angle 0.47003 / 0.29 (11208) hydrogen bonds : bond 0.05554 / 3.66 ( 284) hydrogen bonds : angle 3.66630 / 2.73 ( 623) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.8250 (tpt) cc_final: 0.7993 (tpt) REVERT: A 24 ARG cc_start: 0.8497 (ttp80) cc_final: 0.8239 (ttp-170) REVERT: A 50 GLU cc_start: 0.8350 (pm20) cc_final: 0.7895 (mp0) REVERT: A 68 MET cc_start: 0.8061 (mtt) cc_final: 0.7296 (mtt) REVERT: A 69 SER cc_start: 0.8813 (t) cc_final: 0.8322 (m) REVERT: A 179 LYS cc_start: 0.8285 (tppp) cc_final: 0.7650 (ttpm) REVERT: A 332 GLU cc_start: 0.8337 (tt0) cc_final: 0.8096 (tm-30) REVERT: A 339 HIS cc_start: 0.6716 (t70) cc_final: 0.6288 (t-170) REVERT: A 342 ASP cc_start: 0.8493 (m-30) cc_final: 0.8179 (m-30) REVERT: A 386 SER cc_start: 0.8366 (m) cc_final: 0.8063 (p) outliers start: 2 outliers final: 2 residues processed: 59 average time/residue: 0.8249 time to fit residues: 51.6359 Evaluate side-chains 52 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 378 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.112471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.068989 restraints weight = 28535.821| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.63 r_work: 0.2890 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7566 Z= 0.316 Angle : 0.543 5.386 11208 Z= 0.328 Chirality : 0.041 0.195 1418 Planarity : 0.005 0.037 673 Dihedral : 23.150 167.653 3482 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.04 % Allowed : 14.19 % Favored : 84.78 % 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: 0.12 (0.49), residues: 330 helix: 1.98 (0.53), residues: 113 sheet: -1.84 (0.71), residues: 49 loop : -0.61 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 97 TYR 0.017 0.002 TYR A 5 PHE 0.012 0.001 PHE A 79 TRP 0.004 0.001 TRP A 161 HIS 0.002 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.32 ( 7566) covalent geometry : angle 0.54276 / 0.33 (11208) hydrogen bonds : bond 0.06117 / 4.02 ( 284) hydrogen bonds : angle 3.56465 / 2.64 ( 623) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.8362 (tpt) cc_final: 0.8024 (tpt) REVERT: A 24 ARG cc_start: 0.8526 (ttp80) cc_final: 0.8068 (ttp80) REVERT: A 68 MET cc_start: 0.8219 (mtt) cc_final: 0.7387 (mtt) REVERT: A 69 SER cc_start: 0.8882 (t) cc_final: 0.8356 (m) REVERT: A 179 LYS cc_start: 0.8354 (tppp) cc_final: 0.7689 (ttpm) REVERT: A 332 GLU cc_start: 0.8548 (tt0) cc_final: 0.8260 (tm-30) REVERT: A 339 HIS cc_start: 0.6764 (t70) cc_final: 0.6376 (t-170) REVERT: A 342 ASP cc_start: 0.8513 (m-30) cc_final: 0.8242 (m-30) outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 0.8465 time to fit residues: 47.4763 Evaluate side-chains 50 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 378 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 5 optimal weight: 0.0570 chunk 0 optimal weight: 0.9980 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.114757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.071700 restraints weight = 28411.954| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.48 r_work: 0.2939 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7566 Z= 0.133 Angle : 0.471 5.743 11208 Z= 0.288 Chirality : 0.035 0.197 1418 Planarity : 0.004 0.042 673 Dihedral : 23.283 169.369 3482 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.04 % Allowed : 14.53 % Favored : 84.43 % 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: 0.25 (0.49), residues: 330 helix: 2.14 (0.52), residues: 113 sheet: -1.76 (0.71), residues: 49 loop : -0.56 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 115 TYR 0.010 0.001 TYR A 340 PHE 0.007 0.001 PHE A 79 TRP 0.006 0.002 TRP A 161 HIS 0.001 0.000 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 ( 7566) covalent geometry : angle 0.47129 / 0.29 (11208) hydrogen bonds : bond 0.05027 / 3.38 ( 284) hydrogen bonds : angle 3.33996 / 2.47 ( 623) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8497 (ttp80) cc_final: 0.8236 (ttp-170) REVERT: A 68 MET cc_start: 0.8038 (mtt) cc_final: 0.7199 (mtt) REVERT: A 69 SER cc_start: 0.8885 (t) cc_final: 0.8373 (m) REVERT: A 179 LYS cc_start: 0.8314 (tppp) cc_final: 0.7636 (ttpm) REVERT: A 332 GLU cc_start: 0.8625 (tt0) cc_final: 0.8356 (tm-30) REVERT: A 339 HIS cc_start: 0.6666 (t70) cc_final: 0.6277 (t-170) REVERT: A 342 ASP cc_start: 0.8591 (m-30) cc_final: 0.8281 (m-30) REVERT: A 424 LEU cc_start: 0.8782 (mt) cc_final: 0.8529 (mp) outliers start: 3 outliers final: 3 residues processed: 58 average time/residue: 0.6994 time to fit residues: 43.4281 Evaluate side-chains 53 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 378 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.114606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.071550 restraints weight = 28509.819| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.49 r_work: 0.2935 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7566 Z= 0.162 Angle : 0.465 4.946 11208 Z= 0.286 Chirality : 0.035 0.194 1418 Planarity : 0.004 0.044 673 Dihedral : 23.159 169.842 3482 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.04 % Allowed : 15.57 % Favored : 83.39 % 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: 0.16 (0.49), residues: 330 helix: 1.84 (0.51), residues: 121 sheet: -1.64 (0.72), residues: 49 loop : -0.63 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 115 TYR 0.023 0.002 TYR A 340 PHE 0.008 0.001 PHE A 79 TRP 0.005 0.001 TRP A 161 HIS 0.002 0.000 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 ( 7566) covalent geometry : angle 0.46497 / 0.29 (11208) hydrogen bonds : bond 0.05025 / 3.36 ( 284) hydrogen bonds : angle 3.22917 / 2.39 ( 623) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8511 (ttp80) cc_final: 0.8260 (ttp-170) REVERT: A 69 SER cc_start: 0.8889 (t) cc_final: 0.8370 (m) REVERT: A 86 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7872 (ptm-80) REVERT: A 179 LYS cc_start: 0.8338 (tppp) cc_final: 0.7656 (ttpm) REVERT: A 332 GLU cc_start: 0.8686 (tt0) cc_final: 0.8388 (tm-30) REVERT: A 339 HIS cc_start: 0.6681 (t70) cc_final: 0.6311 (t-170) REVERT: A 342 ASP cc_start: 0.8544 (m-30) cc_final: 0.8258 (m-30) REVERT: A 424 LEU cc_start: 0.8817 (mt) cc_final: 0.8607 (mp) outliers start: 3 outliers final: 3 residues processed: 55 average time/residue: 0.8704 time to fit residues: 50.7434 Evaluate side-chains 52 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 378 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.113727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.070513 restraints weight = 28594.086| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.51 r_work: 0.2914 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7566 Z= 0.211 Angle : 0.480 4.892 11208 Z= 0.294 Chirality : 0.037 0.196 1418 Planarity : 0.004 0.044 673 Dihedral : 23.137 169.388 3482 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.38 % Allowed : 14.88 % Favored : 83.74 % 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: 0.16 (0.49), residues: 330 helix: 1.82 (0.51), residues: 121 sheet: -1.62 (0.73), residues: 49 loop : -0.62 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 97 TYR 0.013 0.002 TYR A 5 PHE 0.009 0.001 PHE A 79 TRP 0.004 0.001 TRP A 161 HIS 0.002 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.21 ( 7566) covalent geometry : angle 0.48000 / 0.29 (11208) hydrogen bonds : bond 0.05164 / 3.43 ( 284) hydrogen bonds : angle 3.20224 / 2.36 ( 623) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8518 (ttp80) cc_final: 0.8279 (ttp-170) REVERT: A 50 GLU cc_start: 0.8397 (pm20) cc_final: 0.8153 (mp0) REVERT: A 68 MET cc_start: 0.8184 (mtt) cc_final: 0.7826 (mmm) REVERT: A 69 SER cc_start: 0.8919 (t) cc_final: 0.8337 (m) REVERT: A 179 LYS cc_start: 0.8356 (tppp) cc_final: 0.7666 (ttpm) REVERT: A 294 HIS cc_start: 0.4800 (OUTLIER) cc_final: 0.4545 (m170) REVERT: A 339 HIS cc_start: 0.6676 (t70) cc_final: 0.6213 (t-170) REVERT: A 342 ASP cc_start: 0.8562 (m-30) cc_final: 0.8259 (m-30) outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.8555 time to fit residues: 48.9168 Evaluate side-chains 52 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 378 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.114070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.070856 restraints weight = 28385.759| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.49 r_work: 0.2928 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7566 Z= 0.181 Angle : 0.469 4.950 11208 Z= 0.288 Chirality : 0.036 0.197 1418 Planarity : 0.004 0.044 673 Dihedral : 23.157 169.627 3482 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.38 % Allowed : 16.26 % Favored : 82.35 % 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: 0.23 (0.49), residues: 330 helix: 1.90 (0.50), residues: 121 sheet: -1.62 (0.72), residues: 49 loop : -0.59 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.016 0.002 TYR A 340 PHE 0.007 0.001 PHE A 79 TRP 0.005 0.001 TRP A 161 HIS 0.001 0.000 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.18 ( 7566) covalent geometry : angle 0.46860 / 0.29 (11208) hydrogen bonds : bond 0.04990 / 3.32 ( 284) hydrogen bonds : angle 3.12910 / 2.31 ( 623) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8513 (ttp80) cc_final: 0.8276 (ttp-170) REVERT: A 68 MET cc_start: 0.8182 (mtt) cc_final: 0.7922 (mmm) REVERT: A 69 SER cc_start: 0.8927 (t) cc_final: 0.8336 (m) REVERT: A 179 LYS cc_start: 0.8352 (tppp) cc_final: 0.7841 (ttpp) REVERT: A 294 HIS cc_start: 0.4757 (OUTLIER) cc_final: 0.4524 (m170) REVERT: A 342 ASP cc_start: 0.8534 (m-30) cc_final: 0.8240 (m-30) outliers start: 4 outliers final: 3 residues processed: 55 average time/residue: 0.9028 time to fit residues: 52.7871 Evaluate side-chains 58 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 378 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.113062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.069441 restraints weight = 28338.363| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.56 r_work: 0.2904 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7566 Z= 0.242 Angle : 0.494 5.014 11208 Z= 0.301 Chirality : 0.038 0.197 1418 Planarity : 0.005 0.043 673 Dihedral : 23.115 169.094 3482 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.38 % Allowed : 15.92 % Favored : 82.70 % 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: 0.31 (0.49), residues: 330 helix: 2.06 (0.51), residues: 115 sheet: -1.62 (0.73), residues: 49 loop : -0.51 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 97 TYR 0.020 0.002 TYR A 340 PHE 0.009 0.001 PHE A 79 TRP 0.004 0.001 TRP A 161 HIS 0.002 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.24 ( 7566) covalent geometry : angle 0.49421 / 0.30 (11208) hydrogen bonds : bond 0.05279 / 3.48 ( 284) hydrogen bonds : angle 3.16446 / 2.34 ( 623) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8273 (ttp-170) REVERT: A 50 GLU cc_start: 0.8396 (pm20) cc_final: 0.8141 (mp0) REVERT: A 68 MET cc_start: 0.8291 (mtt) cc_final: 0.8034 (mmm) REVERT: A 69 SER cc_start: 0.8970 (t) cc_final: 0.8340 (m) REVERT: A 179 LYS cc_start: 0.8355 (tppp) cc_final: 0.7653 (ttpm) REVERT: A 294 HIS cc_start: 0.4744 (OUTLIER) cc_final: 0.4502 (m170) REVERT: A 309 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8567 (mp10) REVERT: A 312 ASP cc_start: 0.8569 (t0) cc_final: 0.8293 (t0) REVERT: A 342 ASP cc_start: 0.8529 (m-30) cc_final: 0.8262 (m-30) outliers start: 4 outliers final: 3 residues processed: 55 average time/residue: 0.9682 time to fit residues: 56.4265 Evaluate side-chains 53 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 378 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.114383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.071112 restraints weight = 28285.588| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.48 r_work: 0.2926 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7566 Z= 0.133 Angle : 0.466 6.110 11208 Z= 0.288 Chirality : 0.034 0.198 1418 Planarity : 0.004 0.042 673 Dihedral : 23.207 169.805 3482 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.38 % Allowed : 16.26 % Favored : 82.35 % 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: 0.41 (0.49), residues: 330 helix: 2.11 (0.51), residues: 115 sheet: -1.55 (0.74), residues: 49 loop : -0.42 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 86 TYR 0.018 0.002 TYR A 340 PHE 0.006 0.001 PHE A 40 TRP 0.005 0.001 TRP A 161 HIS 0.001 0.000 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 ( 7566) covalent geometry : angle 0.46648 / 0.29 (11208) hydrogen bonds : bond 0.04952 / 3.28 ( 284) hydrogen bonds : angle 3.06480 / 2.26 ( 623) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8525 (ttp80) cc_final: 0.8287 (ttp-170) REVERT: A 50 GLU cc_start: 0.8391 (pm20) cc_final: 0.8125 (mp0) REVERT: A 68 MET cc_start: 0.8203 (mtt) cc_final: 0.7966 (mmm) REVERT: A 69 SER cc_start: 0.8958 (t) cc_final: 0.8337 (m) REVERT: A 179 LYS cc_start: 0.8331 (tppp) cc_final: 0.7811 (ttpp) REVERT: A 294 HIS cc_start: 0.4724 (OUTLIER) cc_final: 0.4487 (m170) REVERT: A 309 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8570 (mp10) REVERT: A 312 ASP cc_start: 0.8512 (t0) cc_final: 0.8237 (t0) REVERT: A 342 ASP cc_start: 0.8526 (m-30) cc_final: 0.8252 (m-30) outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 1.0186 time to fit residues: 52.8647 Evaluate side-chains 51 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 378 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.113107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.069639 restraints weight = 28572.135| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.55 r_work: 0.2896 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7566 Z= 0.244 Angle : 0.500 4.997 11208 Z= 0.304 Chirality : 0.038 0.198 1418 Planarity : 0.005 0.043 673 Dihedral : 23.117 169.179 3482 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.38 % Allowed : 16.26 % Favored : 82.35 % 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: 0.36 (0.49), residues: 330 helix: 2.01 (0.51), residues: 115 sheet: -1.52 (0.74), residues: 49 loop : -0.42 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 97 TYR 0.020 0.002 TYR A 340 PHE 0.009 0.001 PHE A 79 TRP 0.003 0.001 TRP A 161 HIS 0.002 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.24 ( 7566) covalent geometry : angle 0.49953 / 0.30 (11208) hydrogen bonds : bond 0.05253 / 3.44 ( 284) hydrogen bonds : angle 3.13095 / 2.31 ( 623) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 660 Ramachandran restraints generated. 330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8512 (ttp80) cc_final: 0.8278 (ttp-170) REVERT: A 50 GLU cc_start: 0.8392 (pm20) cc_final: 0.7967 (mp0) REVERT: A 179 LYS cc_start: 0.8342 (tppp) cc_final: 0.7810 (ttpp) REVERT: A 294 HIS cc_start: 0.4748 (OUTLIER) cc_final: 0.4499 (m170) REVERT: A 312 ASP cc_start: 0.8584 (t0) cc_final: 0.8315 (t0) REVERT: A 342 ASP cc_start: 0.8541 (m-30) cc_final: 0.8270 (m-30) outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 1.0812 time to fit residues: 54.8578 Evaluate side-chains 50 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 378 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.113429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.069943 restraints weight = 28342.237| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.52 r_work: 0.2905 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7566 Z= 0.215 Angle : 0.486 4.905 11208 Z= 0.297 Chirality : 0.037 0.200 1418 Planarity : 0.004 0.042 673 Dihedral : 23.155 169.350 3482 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.38 % Allowed : 15.92 % Favored : 82.70 % 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: 0.40 (0.49), residues: 330 helix: 2.02 (0.51), residues: 115 sheet: -1.48 (0.75), residues: 49 loop : -0.39 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 157 TYR 0.019 0.002 TYR A 340 PHE 0.008 0.001 PHE A 79 TRP 0.003 0.001 TRP A 161 HIS 0.002 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.21 ( 7566) covalent geometry : angle 0.48566 / 0.30 (11208) hydrogen bonds : bond 0.05128 / 3.38 ( 284) hydrogen bonds : angle 3.11332 / 2.28 ( 623) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5301.20 seconds wall clock time: 90 minutes 24.97 seconds (5424.97 seconds total)