Starting phenix.real_space_refine on Wed Aug 5 00:39:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11hx_75706/08_2026/11hx_75706.cif Found real_map, /net/cci-nas-00/data/ceres_data/11hx_75706/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/11hx_75706/08_2026/11hx_75706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11hx_75706/08_2026/11hx_75706.map" model { file = "/net/cci-nas-00/data/ceres_data/11hx_75706/08_2026/11hx_75706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11hx_75706/08_2026/11hx_75706.cif" } 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-2.2rc3-6140/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: 1.57, per 1000 atoms: 0.20 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: 0.47 Conformation dependent library (CDL) restraints added in 221.3 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: 1.01 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: 1.55 Time building geometry restraints manager: 0.66 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: 11228 1.39 - 2.79: 691 2.79 - 4.18: 154 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: 1282 0.095 - 0.190: 205 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: 2.840 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: 0.010 Set scattering table: 0.010 Process input model: 8.700 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.600 ------------------------------------------------------------------------------- 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= 0.458 Angle : 0.761 6.971 12090 Z= 0.598 Chirality : 0.058 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 0.00530 / 0.46 ( 8243) covalent geometry : angle 0.75986 / 0.60 (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 : 0.182 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: 0.7400 (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) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.8512 time to fit residues: 60.9877 Evaluate side-chains 42 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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: 6.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 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: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.102159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.062885 restraints weight = 14762.292| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.68 r_work: 0.2759 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.0808 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= 0.130 Angle : 0.496 6.403 12090 Z= 0.284 Chirality : 0.034 0.254 1490 Planarity : 0.004 0.058 815 Dihedral : 22.973 175.680 3486 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.80 % Allowed : 11.17 % Favored : 88.03 % 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: 1.87 (0.43), residues: 168 sheet: -0.58 (0.56), residues: 79 loop : -0.30 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 33 TYR 0.010 0.001 TYR A 5 PHE 0.013 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 0.00243 / 0.13 ( 8243) covalent geometry : angle 0.49456 / 0.28 (12087) hydrogen bonds : bond 0.04981 / 3.53 ( 318) hydrogen bonds : angle 3.65783 / 2.55 ( 735) metal coordination : bond 0.01508 / 0.75 ( 4) metal coordination : angle 2.60007 / 1.41 ( 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 52 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8471 (mtm110) cc_final: 0.8236 (ttp-110) REVERT: A 37 ARG cc_start: 0.8125 (ptt-90) cc_final: 0.7573 (ptt180) REVERT: A 224 GLU cc_start: 0.9221 (tp30) cc_final: 0.8733 (tp30) REVERT: A 228 MET cc_start: 0.9518 (tpp) cc_final: 0.9216 (tpp) REVERT: A 250 ARG cc_start: 0.8968 (mtm-85) cc_final: 0.7815 (mtm-85) REVERT: A 257 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8697 (p) REVERT: A 291 LYS cc_start: 0.8916 (tttm) cc_final: 0.8513 (mtpp) REVERT: A 361 LYS cc_start: 0.8789 (mppt) cc_final: 0.8572 (mppt) REVERT: A 383 LEU cc_start: 0.8619 (mm) cc_final: 0.7989 (pt) outliers start: 3 outliers final: 1 residues processed: 51 average time/residue: 0.8087 time to fit residues: 43.0681 Evaluate side-chains 47 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 30 optimal weight: 0.0670 chunk 12 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.103086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.064053 restraints weight = 14808.866| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.68 r_work: 0.2792 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1087 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= 0.107 Angle : 0.463 6.837 12090 Z= 0.265 Chirality : 0.032 0.236 1490 Planarity : 0.003 0.033 815 Dihedral : 22.962 175.529 3486 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.86 % Allowed : 11.97 % Favored : 86.17 % 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 (0.43), residues: 431 helix: 2.02 (0.42), residues: 170 sheet: -0.64 (0.56), residues: 84 loop : -0.22 (0.49), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 37 TYR 0.009 0.001 TYR A 5 PHE 0.012 0.001 PHE A 40 TRP 0.003 0.000 TRP A 209 HIS 0.006 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.11 ( 8243) covalent geometry : angle 0.46049 / 0.26 (12087) hydrogen bonds : bond 0.04487 / 3.20 ( 318) hydrogen bonds : angle 3.39159 / 2.39 ( 735) metal coordination : bond 0.01634 / 0.82 ( 4) metal coordination : angle 2.87839 / 1.61 ( 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 : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8719 (ttmm) REVERT: A 224 GLU cc_start: 0.9228 (tp30) cc_final: 0.8745 (tp30) REVERT: A 228 MET cc_start: 0.9505 (tpp) cc_final: 0.9181 (tpp) REVERT: A 250 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.8340 (mpt-90) REVERT: A 257 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8824 (p) REVERT: A 291 LYS cc_start: 0.8915 (tttm) cc_final: 0.8506 (mtpp) REVERT: A 361 LYS cc_start: 0.8820 (mppt) cc_final: 0.8586 (mppt) REVERT: A 383 LEU cc_start: 0.8571 (mm) cc_final: 0.7924 (pt) REVERT: A 416 HIS cc_start: 0.9096 (m90) cc_final: 0.8888 (m90) outliers start: 7 outliers final: 1 residues processed: 54 average time/residue: 0.8022 time to fit residues: 45.2232 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 : 0.192 ------------------------------------------------------------------------------- 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: 0.9980 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.100063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.060570 restraints weight = 14972.641| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.70 r_work: 0.2699 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8247 Z= 0.269 Angle : 0.579 6.782 12090 Z= 0.315 Chirality : 0.041 0.300 1490 Planarity : 0.004 0.056 815 Dihedral : 22.886 175.111 3486 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.60 % Allowed : 13.56 % Favored : 84.84 % 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: 1.93 (0.42), residues: 169 sheet: -0.39 (0.58), residues: 79 loop : -0.29 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 33 TYR 0.012 0.001 TYR A 5 PHE 0.014 0.002 PHE A 196 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 0.00518 / 0.27 ( 8243) covalent geometry : angle 0.57776 / 0.31 (12087) hydrogen bonds : bond 0.05217 / 3.68 ( 318) hydrogen bonds : angle 3.43331 / 2.44 ( 735) metal coordination : bond 0.01085 / 0.54 ( 4) metal coordination : angle 2.45209 / 1.39 ( 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 53 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8531 (mtm110) cc_final: 0.8320 (ttp-110) REVERT: A 219 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8657 (ttmm) REVERT: A 224 GLU cc_start: 0.9222 (tp30) cc_final: 0.8760 (tp30) REVERT: A 228 MET cc_start: 0.9529 (tpp) cc_final: 0.9215 (tpp) REVERT: A 256 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8584 (mm-30) REVERT: A 257 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8856 (p) REVERT: A 291 LYS cc_start: 0.8966 (tttm) cc_final: 0.8560 (mtpp) REVERT: A 355 LYS cc_start: 0.9291 (mmmm) cc_final: 0.9013 (mmmm) REVERT: A 361 LYS cc_start: 0.8898 (mppt) cc_final: 0.8626 (mppt) REVERT: A 383 LEU cc_start: 0.8634 (mm) cc_final: 0.8010 (pt) REVERT: A 416 HIS cc_start: 0.9212 (m90) cc_final: 0.8987 (m90) outliers start: 6 outliers final: 2 residues processed: 51 average time/residue: 0.8318 time to fit residues: 44.2661 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 : 0.196 ------------------------------------------------------------------------------- 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 394 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 7 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.102564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.063634 restraints weight = 14879.428| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.68 r_work: 0.2780 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8247 Z= 0.110 Angle : 0.464 6.969 12090 Z= 0.265 Chirality : 0.032 0.238 1490 Planarity : 0.004 0.036 815 Dihedral : 23.038 175.603 3486 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.60 % Allowed : 15.96 % Favored : 82.45 % 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: 1.98 (0.42), residues: 171 sheet: -0.57 (0.56), residues: 84 loop : -0.24 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.009 0.001 TYR A 5 PHE 0.009 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 0.00214 / 0.11 ( 8243) covalent geometry : angle 0.46252 / 0.26 (12087) hydrogen bonds : bond 0.04372 / 3.10 ( 318) hydrogen bonds : angle 3.27856 / 2.32 ( 735) metal coordination : bond 0.01440 / 0.72 ( 4) metal coordination : angle 2.69846 / 1.53 ( 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 56 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 37 ARG cc_start: 0.7607 (ptt90) cc_final: 0.6874 (mtt180) REVERT: A 72 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8649 (p) REVERT: A 219 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8604 (ttmm) REVERT: A 224 GLU cc_start: 0.9228 (tp30) cc_final: 0.8678 (tp30) REVERT: A 228 MET cc_start: 0.9500 (tpp) cc_final: 0.9145 (tpp) REVERT: A 250 ARG cc_start: 0.8853 (mtm-85) cc_final: 0.8209 (mtm-85) REVERT: A 256 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8280 (mm-30) REVERT: A 257 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8819 (p) REVERT: A 291 LYS cc_start: 0.8904 (tttm) cc_final: 0.8500 (mtpp) REVERT: A 355 LYS cc_start: 0.9268 (mmmm) cc_final: 0.9042 (mmmm) REVERT: A 361 LYS cc_start: 0.8876 (mppt) cc_final: 0.8578 (mppt) REVERT: A 383 LEU cc_start: 0.8566 (mm) cc_final: 0.7929 (pt) REVERT: A 416 HIS cc_start: 0.9227 (m90) cc_final: 0.8915 (m90) outliers start: 6 outliers final: 2 residues processed: 55 average time/residue: 0.7866 time to fit residues: 45.2192 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 : 0.185 ------------------------------------------------------------------------------- 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: 1.9990 chunk 46 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 18 optimal weight: 0.0040 chunk 20 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.102037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.063166 restraints weight = 15102.364| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.68 r_work: 0.2767 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8247 Z= 0.139 Angle : 0.478 7.078 12090 Z= 0.268 Chirality : 0.033 0.250 1490 Planarity : 0.004 0.056 815 Dihedral : 22.964 175.592 3486 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: 0.86 (0.42), residues: 431 helix: 2.03 (0.41), residues: 171 sheet: -0.57 (0.56), residues: 84 loop : -0.23 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 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 0.00268 / 0.14 ( 8243) covalent geometry : angle 0.47685 / 0.27 (12087) hydrogen bonds : bond 0.04400 / 3.13 ( 318) hydrogen bonds : angle 3.23813 / 2.30 ( 735) metal coordination : bond 0.00929 / 0.46 ( 4) metal coordination : angle 2.47233 / 1.42 ( 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 54 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8591 (ttmm) REVERT: A 224 GLU cc_start: 0.9227 (tp30) cc_final: 0.8703 (tp30) REVERT: A 228 MET cc_start: 0.9505 (tpp) cc_final: 0.9152 (tpp) REVERT: A 250 ARG cc_start: 0.8843 (mtm-85) cc_final: 0.8172 (mtm-85) REVERT: A 256 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8292 (mm-30) REVERT: A 257 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8818 (p) REVERT: A 291 LYS cc_start: 0.8905 (tttm) cc_final: 0.8499 (mtpp) REVERT: A 355 LYS cc_start: 0.9285 (mmmm) cc_final: 0.9064 (mmmm) REVERT: A 361 LYS cc_start: 0.8896 (mppt) cc_final: 0.8587 (mppt) REVERT: A 416 HIS cc_start: 0.9232 (m90) cc_final: 0.8912 (m90) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.6864 time to fit residues: 37.9735 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 : 0.109 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 394 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 0.3980 chunk 43 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 39 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.102086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.063251 restraints weight = 14870.138| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.67 r_work: 0.2768 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1272 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= 0.143 Angle : 0.480 7.351 12090 Z= 0.268 Chirality : 0.034 0.251 1490 Planarity : 0.004 0.059 815 Dihedral : 22.964 175.628 3486 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: 0.84 (0.42), residues: 431 helix: 2.04 (0.42), residues: 171 sheet: -0.63 (0.56), residues: 84 loop : -0.24 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 33 TYR 0.009 0.001 TYR A 5 PHE 0.010 0.001 PHE A 196 TRP 0.003 0.001 TRP A 209 HIS 0.002 0.001 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 8243) covalent geometry : angle 0.47825 / 0.27 (12087) hydrogen bonds : bond 0.04370 / 3.11 ( 318) hydrogen bonds : angle 3.22375 / 2.29 ( 735) metal coordination : bond 0.00847 / 0.42 ( 4) metal coordination : angle 2.56873 / 1.50 ( 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 : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8578 (ttmm) REVERT: A 224 GLU cc_start: 0.9216 (tp30) cc_final: 0.8694 (tp30) REVERT: A 228 MET cc_start: 0.9508 (tpp) cc_final: 0.9147 (tpp) REVERT: A 256 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8574 (mm-30) REVERT: A 257 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8825 (p) REVERT: A 291 LYS cc_start: 0.8897 (tttm) cc_final: 0.8486 (mtpp) REVERT: A 355 LYS cc_start: 0.9338 (mmmm) cc_final: 0.9133 (mmmm) REVERT: A 361 LYS cc_start: 0.8917 (mppt) cc_final: 0.8596 (mppt) REVERT: A 383 LEU cc_start: 0.8514 (mm) cc_final: 0.7928 (pt) REVERT: A 416 HIS cc_start: 0.9284 (m90) cc_final: 0.8949 (m90) outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 0.6261 time to fit residues: 35.9813 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 : 0.183 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 394 VAL 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: 2.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.100469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.061056 restraints weight = 14917.507| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.68 r_work: 0.2724 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 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 : 0.004 0.052 8247 Z= 0.229 Angle : 0.555 6.941 12090 Z= 0.303 Chirality : 0.039 0.288 1490 Planarity : 0.004 0.055 815 Dihedral : 22.925 175.658 3486 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.33 % Allowed : 17.29 % 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: 0.80 (0.42), residues: 431 helix: 2.00 (0.42), residues: 171 sheet: -0.57 (0.56), residues: 79 loop : -0.31 (0.48), residues: 181 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 0.014 0.002 PHE A 196 TRP 0.005 0.001 TRP A 209 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.23 ( 8243) covalent geometry : angle 0.55379 / 0.30 (12087) hydrogen bonds : bond 0.04976 / 3.54 ( 318) hydrogen bonds : angle 3.30346 / 2.35 ( 735) metal coordination : bond 0.00894 / 0.44 ( 4) metal coordination : angle 2.53259 / 1.45 ( 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 53 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.9232 (tp30) cc_final: 0.8802 (tp30) REVERT: A 228 MET cc_start: 0.9511 (tpp) cc_final: 0.9163 (tpp) REVERT: A 250 ARG cc_start: 0.8856 (mtm-85) cc_final: 0.8377 (mtm-85) REVERT: A 256 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8578 (mm-30) REVERT: A 257 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8839 (p) REVERT: A 291 LYS cc_start: 0.8932 (tttm) cc_final: 0.8523 (mtpp) REVERT: A 361 LYS cc_start: 0.8976 (mppt) cc_final: 0.8669 (mppt) REVERT: A 383 LEU cc_start: 0.8546 (mm) cc_final: 0.7961 (pt) REVERT: A 416 HIS cc_start: 0.9292 (m90) cc_final: 0.8958 (m90) outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.6605 time to fit residues: 35.9485 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 : 0.165 ------------------------------------------------------------------------------- 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: 5.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.0370 chunk 38 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 0.0670 chunk 59 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.103310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.064451 restraints weight = 15017.595| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.69 r_work: 0.2808 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8247 Z= 0.105 Angle : 0.470 8.219 12090 Z= 0.265 Chirality : 0.032 0.233 1490 Planarity : 0.004 0.060 815 Dihedral : 23.037 176.077 3486 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 0.89 (0.43), residues: 431 helix: 2.12 (0.42), residues: 171 sheet: -0.58 (0.56), residues: 84 loop : -0.27 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 33 TYR 0.009 0.001 TYR A 340 PHE 0.009 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 0.00204 / 0.10 ( 8243) covalent geometry : angle 0.46833 / 0.26 (12087) hydrogen bonds : bond 0.04266 / 3.02 ( 318) hydrogen bonds : angle 3.18859 / 2.26 ( 735) metal coordination : bond 0.01556 / 0.78 ( 4) metal coordination : angle 2.64331 / 1.52 ( 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 56 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.7617 (ptt90) cc_final: 0.6825 (mtt180) REVERT: A 213 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8414 (mpp80) REVERT: A 219 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8561 (ttmm) REVERT: A 224 GLU cc_start: 0.9228 (tp30) cc_final: 0.8720 (tp30) REVERT: A 228 MET cc_start: 0.9499 (tpp) cc_final: 0.9126 (tpp) REVERT: A 257 THR cc_start: 0.9213 (OUTLIER) cc_final: 0.8828 (p) REVERT: A 291 LYS cc_start: 0.8873 (tttm) cc_final: 0.8464 (mtpp) REVERT: A 361 LYS cc_start: 0.8936 (mppt) cc_final: 0.8618 (mppt) REVERT: A 383 LEU cc_start: 0.8466 (mm) cc_final: 0.7892 (pt) REVERT: A 416 HIS cc_start: 0.9254 (m90) cc_final: 0.8920 (m90) outliers start: 5 outliers final: 2 residues processed: 54 average time/residue: 0.6620 time to fit residues: 37.3059 Evaluate side-chains 54 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 213 ARG 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: 6.9990 chunk 46 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.099226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.059652 restraints weight = 14877.997| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.70 r_work: 0.2670 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8247 Z= 0.322 Angle : 0.640 7.353 12090 Z= 0.341 Chirality : 0.044 0.321 1490 Planarity : 0.005 0.058 815 Dihedral : 22.898 175.895 3486 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.06 % Allowed : 18.62 % Favored : 80.32 % 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: 0.72 (0.42), residues: 431 helix: 1.96 (0.42), residues: 169 sheet: -0.55 (0.56), residues: 79 loop : -0.39 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 33 TYR 0.014 0.002 TYR A 305 PHE 0.016 0.002 PHE A 196 TRP 0.004 0.001 TRP A 209 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.32 ( 8243) covalent geometry : angle 0.63756 / 0.34 (12087) hydrogen bonds : bond 0.05511 / 3.93 ( 318) hydrogen bonds : angle 3.38137 / 2.41 ( 735) metal coordination : bond 0.01474 / 0.73 ( 4) metal coordination : angle 3.29207 / 1.85 ( 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 53 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.9225 (tp30) cc_final: 0.8823 (tp30) REVERT: A 228 MET cc_start: 0.9526 (tpp) cc_final: 0.9184 (tpp) REVERT: A 250 ARG cc_start: 0.8756 (mtm-85) cc_final: 0.8240 (mpt-90) REVERT: A 257 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.8877 (p) REVERT: A 291 LYS cc_start: 0.8962 (tttm) cc_final: 0.8552 (mtpp) REVERT: A 361 LYS cc_start: 0.9025 (mppt) cc_final: 0.8712 (mppt) REVERT: A 383 LEU cc_start: 0.8554 (mm) cc_final: 0.7984 (pt) REVERT: A 416 HIS cc_start: 0.9288 (m90) cc_final: 0.8973 (m90) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 0.7252 time to fit residues: 39.3784 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 : 0.135 ------------------------------------------------------------------------------- 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: 0.5980 chunk 34 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 55 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.102211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.063174 restraints weight = 14905.080| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.67 r_work: 0.2759 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1362 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= 0.119 Angle : 0.498 8.155 12090 Z= 0.279 Chirality : 0.033 0.246 1490 Planarity : 0.004 0.063 815 Dihedral : 23.065 176.561 3486 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.80 % Allowed : 19.15 % Favored : 80.05 % 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: 2.07 (0.42), residues: 171 sheet: -0.59 (0.56), residues: 79 loop : -0.38 (0.48), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 33 TYR 0.018 0.001 TYR A 305 PHE 0.010 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 0.00239 / 0.12 ( 8243) covalent geometry : angle 0.49649 / 0.28 (12087) hydrogen bonds : bond 0.04472 / 3.20 ( 318) hydrogen bonds : angle 3.25093 / 2.33 ( 735) metal coordination : bond 0.01403 / 0.70 ( 4) metal coordination : angle 2.56161 / 1.48 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3175.01 seconds wall clock time: 54 minutes 45.35 seconds (3285.35 seconds total)