Starting phenix.real_space_refine on Thu Jul 2 08:16:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11hx_75706/07_2026/11hx_75706.cif Found real_map, /net/cci-nas-00/data/ceres_data/11hx_75706/07_2026/11hx_75706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11hx_75706/07_2026/11hx_75706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11hx_75706/07_2026/11hx_75706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11hx_75706/07_2026/11hx_75706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11hx_75706/07_2026/11hx_75706.map" } resolution = 2.67 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 Zn 1 6.06 5 P 196 5.49 5 Mg 2 5.21 5 S 24 5.16 5 C 4048 2.51 5 N 1433 2.21 5 O 1969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 7673 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3472 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain: "B" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 4033 Classifications: {'RNA': 188} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 13, 'rna3p_pur': 94, 'rna3p_pyr': 65} Link IDs: {'rna2p': 28, 'rna3p': 159} Chain breaks: 1 Chain: "C" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 165 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 6} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1876 SG CYS A 234 82.073 38.342 86.317 1.00184.09 S ATOM 1901 SG CYS A 237 85.188 39.792 87.823 1.00186.49 S ATOM 2128 SG CYS A 265 82.922 37.621 90.008 1.00174.23 S Time building chain proxies: 1.86, per 1000 atoms: 0.24 Number of scatterers: 7673 At special positions: 0 Unit cell: (97.35, 125.4, 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) Zn 1 29.99 S 24 16.00 P 196 15.00 Mg 2 11.99 O 1969 8.00 N 1433 7.00 C 4048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 294.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 268 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 237 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 265 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 234 " Number of angles added : 3 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 816 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 5 sheets defined 41.8% alpha, 15.0% beta 63 base pairs and 110 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 removed outlier: 3.738A pdb=" N ARG A 24 " --> pdb=" O CYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 107 removed outlier: 4.433A 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 182 Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 275 through 294 Processing helix chain 'A' and resid 297 through 314 Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 323 through 334 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 350 removed outlier: 3.907A pdb=" N ALA A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 416 Processing helix chain 'A' and resid 417 through 424 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 4.390A pdb=" N VAL A 6 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 4 " --> pdb=" O PRO A 16 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR A 5 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU A 44 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE A 7 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A 41 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 215 removed outlier: 4.773A pdb=" N SER A 322 " --> pdb=" O TRP A 209 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 55 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL A 190 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 57 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU A 192 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE A 59 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR A 72 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER A 77 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 246 Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.955A pdb=" N ALA A 395 " --> pdb=" O TYR A 387 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 435 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 164 hydrogen bonds 300 hydrogen bond angles 0 basepair planarities 63 basepair parallelities 110 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1312 1.33 - 1.45: 2995 1.45 - 1.57: 3510 1.57 - 1.69: 389 1.69 - 1.80: 37 Bond restraints: 8243 Sorted by residual: bond pdb=" N9 A B 117 " pdb=" C4 A B 117 " ideal model delta sigma weight residual 1.374 1.355 0.019 6.00e-03 2.78e+04 9.65e+00 bond pdb=" N3 A B 117 " pdb=" C4 A B 117 " ideal model delta sigma weight residual 1.344 1.331 0.013 6.00e-03 2.78e+04 4.75e+00 bond pdb=" N7 A B 189 " pdb=" C5 A B 189 " ideal model delta sigma weight residual 1.388 1.375 0.013 6.00e-03 2.78e+04 4.69e+00 bond pdb=" N9 A B 82 " pdb=" C4 A B 82 " ideal model delta sigma weight residual 1.374 1.362 0.012 6.00e-03 2.78e+04 4.34e+00 bond pdb=" N3 C B 49 " pdb=" C4 C B 49 " ideal model delta sigma weight residual 1.335 1.321 0.014 7.00e-03 2.04e+04 4.10e+00 ... (remaining 8238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 11750 1.39 - 2.79: 261 2.79 - 4.18: 62 4.18 - 5.58: 8 5.58 - 6.97: 6 Bond angle restraints: 12087 Sorted by residual: angle pdb=" C1' U B 231 " pdb=" N1 U B 231 " pdb=" C2 U B 231 " ideal model delta sigma weight residual 117.70 124.67 -6.97 1.20e+00 6.94e-01 3.38e+01 angle pdb=" C1' U B 229 " pdb=" N1 U B 229 " pdb=" C2 U B 229 " ideal model delta sigma weight residual 117.70 124.40 -6.70 1.20e+00 6.94e-01 3.12e+01 angle pdb=" N1 U B 231 " pdb=" C2 U B 231 " pdb=" O2 U B 231 " ideal model delta sigma weight residual 122.80 126.35 -3.55 7.00e-01 2.04e+00 2.57e+01 angle pdb=" O2 C B 49 " pdb=" C2 C B 49 " pdb=" N3 C B 49 " ideal model delta sigma weight residual 121.90 118.51 3.39 7.00e-01 2.04e+00 2.35e+01 angle pdb=" N1 U B 229 " pdb=" C2 U B 229 " pdb=" O2 U B 229 " ideal model delta sigma weight residual 122.80 125.96 -3.16 7.00e-01 2.04e+00 2.04e+01 ... (remaining 12082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 4687 34.80 - 69.60: 440 69.60 - 104.41: 61 104.41 - 139.21: 1 139.21 - 174.01: 5 Dihedral angle restraints: 5194 sinusoidal: 3930 harmonic: 1264 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 37.00 163.00 1 1.50e+01 4.44e-03 8.35e+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 57.99 174.01 1 1.70e+01 3.46e-03 6.63e+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 26.17 -154.17 1 1.70e+01 3.46e-03 6.31e+01 ... (remaining 5191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1454 0.095 - 0.190: 33 0.190 - 0.285: 2 0.285 - 0.380: 0 0.380 - 0.475: 1 Chirality restraints: 1490 Sorted by residual: chirality pdb=" P U B 97 " pdb=" OP1 U B 97 " pdb=" OP2 U B 97 " pdb=" O5' U B 97 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" CB ILE A 145 " pdb=" CA ILE A 145 " pdb=" CG1 ILE A 145 " pdb=" CG2 ILE A 145 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C3' A B 86 " pdb=" C4' A B 86 " pdb=" O3' A B 86 " pdb=" C2' A B 86 " both_signs ideal model delta sigma weight residual False -2.48 -2.27 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1487 not shown) Planarity restraints: 815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 80 " 0.029 2.00e-02 2.50e+03 1.25e-02 4.66e+00 pdb=" N9 G B 80 " -0.030 2.00e-02 2.50e+03 pdb=" C8 G B 80 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G B 80 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G B 80 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 80 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G B 80 " 0.010 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 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G B 80 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G B 80 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 56 " -0.024 2.00e-02 2.50e+03 1.09e-02 3.27e+00 pdb=" N9 A B 56 " 0.024 2.00e-02 2.50e+03 pdb=" C8 A B 56 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A B 56 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A B 56 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 56 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A B 56 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A B 56 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A B 56 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 56 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A B 56 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 7 " -0.023 2.00e-02 2.50e+03 9.97e-03 2.98e+00 pdb=" N9 G B 7 " 0.024 2.00e-02 2.50e+03 pdb=" C8 G B 7 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B 7 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G B 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 7 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G B 7 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G B 7 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 7 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B 7 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 7 " 0.001 2.00e-02 2.50e+03 ... (remaining 812 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 73 2.61 - 3.18: 6245 3.18 - 3.75: 15158 3.75 - 4.33: 19692 4.33 - 4.90: 27485 Nonbonded interactions: 68653 Sorted by model distance: nonbonded pdb=" NE2 HIS A 273 " pdb="MG MG A 502 " model vdw 2.032 2.250 nonbonded pdb=" ND1 HIS A 245 " pdb="MG MG A 502 " model vdw 2.062 2.250 nonbonded pdb=" OD1 ASP A 60 " pdb="MG MG A 503 " model vdw 2.088 2.170 nonbonded pdb=" OE1 GLU A 192 " pdb="MG MG A 503 " model vdw 2.254 2.170 nonbonded pdb=" SG CYS A 237 " pdb=" CE1 HIS A 268 " model vdw 2.509 2.896 ... (remaining 68648 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: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.580 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:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 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 : 0.005 0.042 8247 Z= 0.428 Angle : 0.560 6.971 12090 Z= 0.450 Chirality : 0.037 0.475 1490 Planarity : 0.004 0.034 815 Dihedral : 21.922 174.010 4378 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: 0.21 (0.41), residues: 431 helix: 1.29 (0.42), residues: 166 sheet: -0.80 (0.55), residues: 79 loop : -0.37 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 115 TYR 0.011 0.001 TYR A 5 PHE 0.016 0.002 PHE A 40 TRP 0.005 0.001 TRP A 209 HIS 0.005 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.43 ( 8243) covalent geometry : angle 0.55879 / 0.45 (12087) hydrogen bonds : bond 0.10100 / 6.98 ( 318) hydrogen bonds : angle 4.75382 / 3.26 ( 735) metal coordination : bond 0.00581 / 0.28 ( 4) metal coordination : angle 2.16396 / 1.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8413 (tp30) cc_final: 0.8114 (tm-30) REVERT: A 37 ARG cc_start: 0.8135 (ptt-90) cc_final: 0.7350 (ptt180) REVERT: A 224 GLU cc_start: 0.9178 (tp30) cc_final: 0.8658 (tp30) REVERT: A 228 MET cc_start: 0.9515 (tpp) cc_final: 0.9215 (tpp) REVERT: A 291 LYS cc_start: 0.8901 (tttm) cc_final: 0.8506 (mtpp) REVERT: A 372 ARG cc_start: 0.8578 (mmm160) cc_final: 0.8352 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.7760 time to fit residues: 55.5619 Evaluate side-chains 43 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.101675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.062330 restraints weight = 14770.747| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.68 r_work: 0.2767 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8247 Z= 0.156 Angle : 0.482 6.561 12090 Z= 0.280 Chirality : 0.034 0.197 1490 Planarity : 0.004 0.060 815 Dihedral : 23.045 175.664 3486 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.80 % Allowed : 10.90 % Favored : 88.30 % 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: 0.70 (0.42), residues: 431 helix: 1.88 (0.43), residues: 168 sheet: -0.59 (0.56), residues: 79 loop : -0.30 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 33 TYR 0.011 0.001 TYR A 5 PHE 0.014 0.001 PHE A 40 TRP 0.005 0.001 TRP A 209 HIS 0.006 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 ( 8243) covalent geometry : angle 0.48017 / 0.28 (12087) hydrogen bonds : bond 0.04816 / 3.39 ( 318) hydrogen bonds : angle 3.65126 / 2.55 ( 735) metal coordination : bond 0.01447 / 0.72 ( 4) metal coordination : angle 2.52704 / 1.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8474 (mtm110) cc_final: 0.8235 (ttp-110) REVERT: A 37 ARG cc_start: 0.8115 (ptt-90) cc_final: 0.7879 (ptt90) REVERT: A 219 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8779 (ttmm) REVERT: A 224 GLU cc_start: 0.9220 (tp30) cc_final: 0.8735 (tp30) REVERT: A 228 MET cc_start: 0.9526 (tpp) cc_final: 0.9221 (tpp) REVERT: A 250 ARG cc_start: 0.8978 (mtm-85) cc_final: 0.7841 (mtm-85) REVERT: A 257 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8682 (p) REVERT: A 291 LYS cc_start: 0.8931 (tttm) cc_final: 0.8529 (mtpp) REVERT: A 361 LYS cc_start: 0.8789 (mppt) cc_final: 0.8569 (mppt) REVERT: A 372 ARG cc_start: 0.8641 (mmm160) cc_final: 0.8402 (mmm-85) REVERT: A 383 LEU cc_start: 0.8611 (mm) cc_final: 0.7981 (pt) outliers start: 3 outliers final: 1 residues processed: 52 average time/residue: 0.7096 time to fit residues: 38.5238 Evaluate side-chains 49 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 421 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 27 optimal weight: 5.9990 chunk 30 optimal weight: 0.1980 chunk 12 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.0010 chunk 49 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.102976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.063904 restraints weight = 14837.030| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.68 r_work: 0.2789 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8247 Z= 0.111 Angle : 0.446 6.943 12090 Z= 0.261 Chirality : 0.032 0.185 1490 Planarity : 0.003 0.033 815 Dihedral : 23.060 176.758 3486 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.86 % Allowed : 12.50 % Favored : 85.64 % 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: 0.81 (0.43), residues: 431 helix: 2.05 (0.42), residues: 170 sheet: -0.68 (0.55), residues: 84 loop : -0.26 (0.49), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 250 TYR 0.008 0.001 TYR A 5 PHE 0.014 0.001 PHE A 40 TRP 0.003 0.000 TRP A 209 HIS 0.005 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 ( 8243) covalent geometry : angle 0.44392 / 0.26 (12087) hydrogen bonds : bond 0.04263 / 3.03 ( 318) hydrogen bonds : angle 3.38829 / 2.39 ( 735) metal coordination : bond 0.01763 / 0.88 ( 4) metal coordination : angle 2.94970 / 1.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8782 (ttmm) REVERT: A 224 GLU cc_start: 0.9229 (tp30) cc_final: 0.8747 (tp30) REVERT: A 228 MET cc_start: 0.9501 (tpp) cc_final: 0.9171 (tpp) REVERT: A 250 ARG cc_start: 0.8825 (mtm-85) cc_final: 0.8302 (mpt-90) REVERT: A 257 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8832 (p) REVERT: A 291 LYS cc_start: 0.8912 (tttm) cc_final: 0.8505 (mtpp) REVERT: A 361 LYS cc_start: 0.8834 (mppt) cc_final: 0.8592 (mppt) REVERT: A 383 LEU cc_start: 0.8567 (mm) cc_final: 0.7926 (pt) outliers start: 7 outliers final: 1 residues processed: 55 average time/residue: 0.7353 time to fit residues: 42.1774 Evaluate side-chains 51 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 257 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 3 optimal weight: 0.0270 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.101401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.062110 restraints weight = 15036.438| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.70 r_work: 0.2754 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8247 Z= 0.182 Angle : 0.468 6.521 12090 Z= 0.271 Chirality : 0.034 0.203 1490 Planarity : 0.004 0.058 815 Dihedral : 22.982 176.677 3486 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.60 % Allowed : 14.36 % Favored : 84.04 % 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: 0.82 (0.42), residues: 431 helix: 2.01 (0.42), residues: 170 sheet: -0.63 (0.56), residues: 84 loop : -0.23 (0.49), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 33 TYR 0.010 0.001 TYR A 5 PHE 0.011 0.001 PHE A 196 TRP 0.004 0.001 TRP A 209 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 ( 8243) covalent geometry : angle 0.46646 / 0.27 (12087) hydrogen bonds : bond 0.04480 / 3.17 ( 318) hydrogen bonds : angle 3.32816 / 2.36 ( 735) metal coordination : bond 0.00851 / 0.42 ( 4) metal coordination : angle 2.34196 / 1.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8471 (mtm110) cc_final: 0.8257 (ttp-110) REVERT: A 37 ARG cc_start: 0.7705 (ptt90) cc_final: 0.7188 (mtm180) REVERT: A 224 GLU cc_start: 0.9234 (tp30) cc_final: 0.8755 (tp30) REVERT: A 228 MET cc_start: 0.9513 (tpp) cc_final: 0.9184 (tpp) REVERT: A 250 ARG cc_start: 0.8868 (mtm-85) cc_final: 0.8310 (mtm-85) REVERT: A 256 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8277 (mm-30) REVERT: A 257 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8797 (p) REVERT: A 291 LYS cc_start: 0.8908 (tttm) cc_final: 0.8504 (mtpp) REVERT: A 355 LYS cc_start: 0.9296 (mmmm) cc_final: 0.9002 (mmmm) REVERT: A 361 LYS cc_start: 0.8876 (mppt) cc_final: 0.8595 (mppt) REVERT: A 383 LEU cc_start: 0.8588 (mm) cc_final: 0.7963 (pt) outliers start: 6 outliers final: 2 residues processed: 53 average time/residue: 0.6950 time to fit residues: 38.4856 Evaluate side-chains 49 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 394 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.0470 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.102425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.063468 restraints weight = 14879.985| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.67 r_work: 0.2786 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8247 Z= 0.126 Angle : 0.441 7.011 12090 Z= 0.257 Chirality : 0.032 0.190 1490 Planarity : 0.003 0.034 815 Dihedral : 23.032 176.822 3486 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.60 % Allowed : 15.43 % Favored : 82.98 % 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: 0.86 (0.42), residues: 431 helix: 2.08 (0.42), residues: 170 sheet: -0.59 (0.56), residues: 84 loop : -0.26 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 33 TYR 0.009 0.001 TYR A 5 PHE 0.009 0.001 PHE A 196 TRP 0.003 0.000 TRP A 209 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 ( 8243) covalent geometry : angle 0.43922 / 0.26 (12087) hydrogen bonds : bond 0.04165 / 2.96 ( 318) hydrogen bonds : angle 3.25277 / 2.30 ( 735) metal coordination : bond 0.01178 / 0.59 ( 4) metal coordination : angle 2.55577 / 1.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8663 (p) REVERT: A 219 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8658 (ttmm) REVERT: A 224 GLU cc_start: 0.9222 (tp30) cc_final: 0.8689 (tp30) REVERT: A 228 MET cc_start: 0.9504 (tpp) cc_final: 0.9151 (tpp) REVERT: A 256 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8574 (mm-30) REVERT: A 257 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8808 (p) REVERT: A 291 LYS cc_start: 0.8902 (tttm) cc_final: 0.8497 (mtpp) REVERT: A 355 LYS cc_start: 0.9295 (mmmm) cc_final: 0.9081 (mmmm) REVERT: A 361 LYS cc_start: 0.8868 (mppt) cc_final: 0.8566 (mppt) REVERT: A 383 LEU cc_start: 0.8564 (mm) cc_final: 0.7931 (pt) outliers start: 6 outliers final: 2 residues processed: 54 average time/residue: 0.7054 time to fit residues: 39.8291 Evaluate side-chains 52 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 394 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 21 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 18 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.099172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.059489 restraints weight = 15020.073| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.94 r_work: 0.2674 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8247 Z= 0.330 Angle : 0.558 6.151 12090 Z= 0.320 Chirality : 0.040 0.228 1490 Planarity : 0.005 0.047 815 Dihedral : 22.936 176.412 3486 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.33 % Allowed : 16.49 % Favored : 82.18 % 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: 0.80 (0.42), residues: 431 helix: 1.94 (0.42), residues: 169 sheet: -0.39 (0.58), residues: 74 loop : -0.34 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 33 TYR 0.013 0.002 TYR A 305 PHE 0.016 0.002 PHE A 196 TRP 0.007 0.001 TRP A 209 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.33 ( 8243) covalent geometry : angle 0.55673 / 0.32 (12087) hydrogen bonds : bond 0.05378 / 3.77 ( 318) hydrogen bonds : angle 3.40647 / 2.43 ( 735) metal coordination : bond 0.01621 / 0.80 ( 4) metal coordination : angle 2.69348 / 1.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8591 (ttmm) REVERT: A 224 GLU cc_start: 0.9234 (tp30) cc_final: 0.8803 (tp30) REVERT: A 228 MET cc_start: 0.9527 (tpp) cc_final: 0.9203 (tpp) REVERT: A 250 ARG cc_start: 0.8855 (mtm-85) cc_final: 0.8375 (mtm-85) REVERT: A 256 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8591 (mm-30) REVERT: A 257 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8861 (p) REVERT: A 291 LYS cc_start: 0.8962 (tttm) cc_final: 0.8558 (mtpp) REVERT: A 355 LYS cc_start: 0.9299 (mmmm) cc_final: 0.9094 (mmmm) REVERT: A 361 LYS cc_start: 0.8953 (mppt) cc_final: 0.8648 (mppt) outliers start: 5 outliers final: 2 residues processed: 52 average time/residue: 0.7091 time to fit residues: 38.5773 Evaluate side-chains 50 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 321 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 0.0050 chunk 39 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.101881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.062661 restraints weight = 14825.478| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.68 r_work: 0.2748 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8247 Z= 0.128 Angle : 0.461 7.213 12090 Z= 0.267 Chirality : 0.033 0.192 1490 Planarity : 0.004 0.051 815 Dihedral : 23.088 177.106 3486 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.86 % Allowed : 16.76 % Favored : 81.38 % 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: 0.79 (0.42), residues: 431 helix: 2.01 (0.41), residues: 171 sheet: -0.63 (0.56), residues: 79 loop : -0.32 (0.48), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 33 TYR 0.009 0.001 TYR A 5 PHE 0.011 0.001 PHE A 40 TRP 0.005 0.001 TRP A 209 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 ( 8243) covalent geometry : angle 0.45933 / 0.27 (12087) hydrogen bonds : bond 0.04229 / 3.01 ( 318) hydrogen bonds : angle 3.26051 / 2.31 ( 735) metal coordination : bond 0.01129 / 0.56 ( 4) metal coordination : angle 2.37542 / 1.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8573 (ttmm) REVERT: A 224 GLU cc_start: 0.9230 (tp30) cc_final: 0.8717 (tp30) REVERT: A 228 MET cc_start: 0.9510 (tpp) cc_final: 0.9153 (tpp) REVERT: A 250 ARG cc_start: 0.8854 (mtm-85) cc_final: 0.8189 (mtm-85) REVERT: A 256 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8210 (mm-30) REVERT: A 257 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.8856 (p) REVERT: A 291 LYS cc_start: 0.8900 (tttm) cc_final: 0.8494 (mtpp) REVERT: A 355 LYS cc_start: 0.9299 (mmmm) cc_final: 0.9074 (mmmm) REVERT: A 361 LYS cc_start: 0.8927 (mppt) cc_final: 0.8603 (mppt) REVERT: A 372 ARG cc_start: 0.8686 (mmm160) cc_final: 0.8432 (mmm-85) REVERT: A 383 LEU cc_start: 0.8525 (mm) cc_final: 0.7927 (pt) outliers start: 7 outliers final: 2 residues processed: 55 average time/residue: 0.7642 time to fit residues: 43.9987 Evaluate side-chains 51 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 321 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.099863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.060326 restraints weight = 14937.125| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 1.84 r_work: 0.2693 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8247 Z= 0.263 Angle : 0.521 6.804 12090 Z= 0.299 Chirality : 0.037 0.221 1490 Planarity : 0.004 0.051 815 Dihedral : 22.997 176.893 3486 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.06 % Allowed : 17.55 % Favored : 81.38 % 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: 0.76 (0.42), residues: 431 helix: 1.98 (0.42), residues: 169 sheet: -0.56 (0.56), residues: 79 loop : -0.34 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 33 TYR 0.011 0.001 TYR A 5 PHE 0.013 0.002 PHE A 196 TRP 0.005 0.001 TRP A 209 HIS 0.002 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.26 ( 8243) covalent geometry : angle 0.51970 / 0.30 (12087) hydrogen bonds : bond 0.04959 / 3.51 ( 318) hydrogen bonds : angle 3.32333 / 2.37 ( 735) metal coordination : bond 0.01011 / 0.50 ( 4) metal coordination : angle 2.57103 / 1.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.9229 (tp30) cc_final: 0.8803 (tp30) REVERT: A 228 MET cc_start: 0.9523 (tpp) cc_final: 0.9193 (tpp) REVERT: A 256 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8583 (mm-30) REVERT: A 257 THR cc_start: 0.9281 (OUTLIER) cc_final: 0.8889 (p) REVERT: A 291 LYS cc_start: 0.8948 (tttm) cc_final: 0.8540 (mtpp) REVERT: A 361 LYS cc_start: 0.8962 (mppt) cc_final: 0.8656 (mppt) REVERT: A 383 LEU cc_start: 0.8567 (mm) cc_final: 0.7983 (pt) outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.7899 time to fit residues: 41.2508 Evaluate side-chains 50 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 321 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 30 optimal weight: 0.0870 chunk 59 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.102059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.062970 restraints weight = 14936.959| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.68 r_work: 0.2755 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8247 Z= 0.118 Angle : 0.466 7.949 12090 Z= 0.269 Chirality : 0.032 0.192 1490 Planarity : 0.004 0.059 815 Dihedral : 23.101 177.430 3486 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.33 % Allowed : 17.55 % Favored : 81.12 % 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: 0.83 (0.42), residues: 431 helix: 2.07 (0.42), residues: 171 sheet: -0.57 (0.57), residues: 79 loop : -0.35 (0.48), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 33 TYR 0.009 0.001 TYR A 5 PHE 0.010 0.001 PHE A 40 TRP 0.004 0.001 TRP A 209 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 ( 8243) covalent geometry : angle 0.46437 / 0.27 (12087) hydrogen bonds : bond 0.04222 / 3.01 ( 318) hydrogen bonds : angle 3.23853 / 2.30 ( 735) metal coordination : bond 0.01258 / 0.63 ( 4) metal coordination : angle 2.60308 / 1.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8577 (ttmm) REVERT: A 224 GLU cc_start: 0.9220 (tp30) cc_final: 0.8713 (tp30) REVERT: A 228 MET cc_start: 0.9512 (tpp) cc_final: 0.9160 (tpp) REVERT: A 250 ARG cc_start: 0.8879 (mtm-85) cc_final: 0.8421 (mtm-85) REVERT: A 256 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8570 (mm-30) REVERT: A 257 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8889 (p) REVERT: A 291 LYS cc_start: 0.8912 (tttm) cc_final: 0.8506 (mtpp) REVERT: A 361 LYS cc_start: 0.8956 (mppt) cc_final: 0.8658 (mppt) REVERT: A 372 ARG cc_start: 0.8729 (mmm160) cc_final: 0.8469 (mmm-85) REVERT: A 383 LEU cc_start: 0.8523 (mm) cc_final: 0.7946 (pt) REVERT: A 416 HIS cc_start: 0.9248 (m90) cc_final: 0.9020 (m90) outliers start: 5 outliers final: 2 residues processed: 52 average time/residue: 0.7102 time to fit residues: 38.6797 Evaluate side-chains 52 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 321 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.099295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.059711 restraints weight = 14903.289| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.90 r_work: 0.2669 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8247 Z= 0.314 Angle : 0.556 6.960 12090 Z= 0.317 Chirality : 0.039 0.228 1490 Planarity : 0.004 0.058 815 Dihedral : 22.974 176.986 3486 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.06 % Allowed : 18.09 % Favored : 80.85 % 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: 0.73 (0.42), residues: 431 helix: 1.99 (0.42), residues: 169 sheet: -0.55 (0.57), residues: 79 loop : -0.42 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 33 TYR 0.013 0.002 TYR A 305 PHE 0.015 0.002 PHE A 196 TRP 0.004 0.001 TRP A 209 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.31 ( 8243) covalent geometry : angle 0.55494 / 0.32 (12087) hydrogen bonds : bond 0.05273 / 3.73 ( 318) hydrogen bonds : angle 3.36594 / 2.40 ( 735) metal coordination : bond 0.01361 / 0.67 ( 4) metal coordination : angle 2.59535 / 1.44 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.9218 (tp30) cc_final: 0.8809 (tp30) REVERT: A 228 MET cc_start: 0.9523 (tpp) cc_final: 0.9193 (tpp) REVERT: A 250 ARG cc_start: 0.8871 (mtm-85) cc_final: 0.8378 (mtm-85) REVERT: A 256 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8595 (mm-30) REVERT: A 257 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8887 (p) REVERT: A 291 LYS cc_start: 0.8959 (tttm) cc_final: 0.8550 (mtpp) REVERT: A 361 LYS cc_start: 0.9029 (mppt) cc_final: 0.8731 (mppt) REVERT: A 383 LEU cc_start: 0.8557 (mm) cc_final: 0.7973 (pt) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.7486 time to fit residues: 39.1331 Evaluate side-chains 49 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 321 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.101368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.062127 restraints weight = 14888.637| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.68 r_work: 0.2737 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8247 Z= 0.143 Angle : 0.478 7.848 12090 Z= 0.275 Chirality : 0.033 0.197 1490 Planarity : 0.004 0.062 815 Dihedral : 23.096 177.565 3486 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.80 % Allowed : 18.09 % Favored : 81.12 % 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: 0.81 (0.42), residues: 431 helix: 2.06 (0.41), residues: 171 sheet: -0.52 (0.57), residues: 79 loop : -0.40 (0.47), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 33 TYR 0.009 0.001 TYR A 5 PHE 0.011 0.001 PHE A 40 TRP 0.005 0.001 TRP A 209 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 8243) covalent geometry : angle 0.47655 / 0.27 (12087) hydrogen bonds : bond 0.04344 / 3.11 ( 318) hydrogen bonds : angle 3.26430 / 2.32 ( 735) metal coordination : bond 0.01075 / 0.53 ( 4) metal coordination : angle 2.26316 / 1.30 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3117.12 seconds wall clock time: 53 minutes 49.61 seconds (3229.61 seconds total)