Starting phenix.real_space_refine on Sat Apr 4 20:09:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iua_60895/04_2026/9iua_60895.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iua_60895/04_2026/9iua_60895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iua_60895/04_2026/9iua_60895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iua_60895/04_2026/9iua_60895.map" model { file = "/net/cci-nas-00/data/ceres_data/9iua_60895/04_2026/9iua_60895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iua_60895/04_2026/9iua_60895.cif" } resolution = 3.78 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 36 5.49 5 S 9 5.16 5 C 1238 2.51 5 N 402 2.21 5 O 468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2154 Number of models: 1 Model: "" Number of chains: 4 Chain: "G1" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "H1" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 368 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1415 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain breaks: 3 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1425 SG CYS C 304 33.951 42.017 16.994 1.00198.50 S ATOM 1443 SG CYS C 307 33.730 38.218 16.696 1.00196.64 S ATOM 1594 SG CYS C 326 35.896 39.210 18.793 1.00188.29 S ATOM 1666 SG CYS C 335 36.869 40.318 15.310 1.00202.76 S Time building chain proxies: 0.77, per 1000 atoms: 0.36 Number of scatterers: 2154 At special positions: 0 Unit cell: (77.6048, 74.0773, 50.5607, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 9 16.00 P 36 15.00 O 468 8.00 N 402 7.00 C 1238 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: 0.29 Conformation dependent library (CDL) restraints added in 59.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 326 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 335 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 307 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 304 " Number of angles added : 6 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 330 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 2 sheets defined 50.8% alpha, 9.6% beta 18 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 197 through 208 Processing helix chain 'C' and resid 212 through 217 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 342 through 357 Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 478 through 486 Processing sheet with id=AA1, first strand: chain 'C' and resid 302 through 304 Processing sheet with id=AA2, first strand: chain 'C' and resid 311 through 314 69 hydrogen bonds defined for protein. 192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 0.35 Time building geometry restraints manager: 0.31 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: 440 1.33 - 1.45: 756 1.45 - 1.57: 991 1.57 - 1.69: 70 1.69 - 1.81: 13 Bond restraints: 2270 Sorted by residual: bond pdb=" CA SER C 212 " pdb=" CB SER C 212 " ideal model delta sigma weight residual 1.526 1.480 0.046 1.53e-02 4.27e+03 9.04e+00 bond pdb=" CA SER C 238 " pdb=" CB SER C 238 " ideal model delta sigma weight residual 1.528 1.485 0.043 1.59e-02 3.96e+03 7.30e+00 bond pdb=" CA SER C 296 " pdb=" CB SER C 296 " ideal model delta sigma weight residual 1.530 1.493 0.036 1.43e-02 4.89e+03 6.47e+00 bond pdb=" P DGG1 1 " pdb=" OP2 DGG1 1 " ideal model delta sigma weight residual 1.480 1.530 -0.050 2.00e-02 2.50e+03 6.13e+00 bond pdb=" P DGG1 1 " pdb=" OP1 DGG1 1 " ideal model delta sigma weight residual 1.480 1.529 -0.049 2.00e-02 2.50e+03 6.13e+00 ... (remaining 2265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 2777 2.41 - 4.81: 347 4.81 - 7.21: 65 7.21 - 9.62: 19 9.62 - 12.02: 7 Bond angle restraints: 3215 Sorted by residual: angle pdb=" O3' DGH1 32 " pdb=" P DTH1 33 " pdb=" O5' DTH1 33 " ideal model delta sigma weight residual 104.00 91.98 12.02 1.50e+00 4.44e-01 6.43e+01 angle pdb=" O3' DGH1 35 " pdb=" P DAH1 36 " pdb=" O5' DAH1 36 " ideal model delta sigma weight residual 104.00 92.30 11.70 1.50e+00 4.44e-01 6.09e+01 angle pdb=" O3' DTH1 33 " pdb=" P DCH1 34 " pdb=" O5' DCH1 34 " ideal model delta sigma weight residual 104.00 93.14 10.86 1.50e+00 4.44e-01 5.24e+01 angle pdb=" C1' DGH1 29 " pdb=" N9 DGH1 29 " pdb=" C8 DGH1 29 " ideal model delta sigma weight residual 127.00 137.02 -10.02 1.50e+00 4.44e-01 4.47e+01 angle pdb=" C1' DGH1 29 " pdb=" N9 DGH1 29 " pdb=" C4 DGH1 29 " ideal model delta sigma weight residual 127.00 117.15 9.85 1.50e+00 4.44e-01 4.31e+01 ... (remaining 3210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 867 15.39 - 30.77: 169 30.77 - 46.16: 104 46.16 - 61.55: 95 61.55 - 76.93: 8 Dihedral angle restraints: 1243 sinusoidal: 735 harmonic: 508 Sorted by residual: dihedral pdb=" CA LEU C 282 " pdb=" C LEU C 282 " pdb=" N VAL C 283 " pdb=" CA VAL C 283 " ideal model delta harmonic sigma weight residual -180.00 -141.68 -38.32 0 5.00e+00 4.00e-02 5.87e+01 dihedral pdb=" C TYR C 216 " pdb=" N TYR C 216 " pdb=" CA TYR C 216 " pdb=" CB TYR C 216 " ideal model delta harmonic sigma weight residual -122.60 -134.26 11.66 0 2.50e+00 1.60e-01 2.18e+01 dihedral pdb=" C HIS C 199 " pdb=" N HIS C 199 " pdb=" CA HIS C 199 " pdb=" CB HIS C 199 " ideal model delta harmonic sigma weight residual -122.60 -134.01 11.41 0 2.50e+00 1.60e-01 2.08e+01 ... (remaining 1240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 310 0.138 - 0.275: 37 0.275 - 0.413: 6 0.413 - 0.551: 0 0.551 - 0.688: 2 Chirality restraints: 355 Sorted by residual: chirality pdb=" P DGH1 29 " pdb=" OP1 DGH1 29 " pdb=" OP2 DGH1 29 " pdb=" O5' DGH1 29 " both_signs ideal model delta sigma weight residual True 2.35 -3.03 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" P DGG1 1 " pdb=" OP1 DGG1 1 " pdb=" OP2 DGG1 1 " pdb=" O5' DGG1 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DCH1 37 " pdb=" OP1 DCH1 37 " pdb=" OP2 DCH1 37 " pdb=" O5' DCH1 37 " both_signs ideal model delta sigma weight residual True 2.35 -2.73 -0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 352 not shown) Planarity restraints: 286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DGH1 32 " -0.056 2.00e-02 2.50e+03 2.68e-02 2.15e+01 pdb=" N9 DGH1 32 " 0.058 2.00e-02 2.50e+03 pdb=" C8 DGH1 32 " 0.020 2.00e-02 2.50e+03 pdb=" N7 DGH1 32 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DGH1 32 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DGH1 32 " -0.015 2.00e-02 2.50e+03 pdb=" O6 DGH1 32 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DGH1 32 " -0.019 2.00e-02 2.50e+03 pdb=" C2 DGH1 32 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DGH1 32 " 0.029 2.00e-02 2.50e+03 pdb=" N3 DGH1 32 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DGH1 32 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 461 " 0.364 9.50e-02 1.11e+02 1.64e-01 1.85e+01 pdb=" NE ARG C 461 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG C 461 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG C 461 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 461 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DGG1 16 " 0.051 2.00e-02 2.50e+03 2.45e-02 1.81e+01 pdb=" N9 DGG1 16 " -0.047 2.00e-02 2.50e+03 pdb=" C8 DGG1 16 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DGG1 16 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DGG1 16 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DGG1 16 " 0.019 2.00e-02 2.50e+03 pdb=" O6 DGG1 16 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DGG1 16 " 0.013 2.00e-02 2.50e+03 pdb=" C2 DGG1 16 " -0.020 2.00e-02 2.50e+03 pdb=" N2 DGG1 16 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DGG1 16 " -0.025 2.00e-02 2.50e+03 pdb=" C4 DGG1 16 " -0.019 2.00e-02 2.50e+03 ... (remaining 283 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 449 2.80 - 3.33: 1946 3.33 - 3.85: 4085 3.85 - 4.38: 4547 4.38 - 4.90: 6813 Nonbonded interactions: 17840 Sorted by model distance: nonbonded pdb=" NH1 ARG C 323 " pdb=" OG1 THR C 339 " model vdw 2.275 3.120 nonbonded pdb=" OP2 DCG1 12 " pdb=" NZ LYS C 236 " model vdw 2.367 3.120 nonbonded pdb=" O5' DCG1 18 " pdb=" O4' DCG1 18 " model vdw 2.451 2.432 nonbonded pdb=" OP2 DGH1 35 " pdb=" OH TYR C 312 " model vdw 2.471 3.040 nonbonded pdb=" O LEU C 297 " pdb=" ND2 ASN C 452 " model vdw 2.493 3.120 ... (remaining 17835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.270 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 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 : 0.010 0.056 2274 Z= 0.554 Angle : 1.899 21.763 3221 Z= 1.120 Chirality : 0.105 0.688 355 Planarity : 0.020 0.164 286 Dihedral : 24.967 76.932 913 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.59 % Allowed : 2.96 % Favored : 96.45 % Rotamer: Outliers : 8.67 % Allowed : 10.00 % Favored : 81.33 % Cbeta Deviations : 1.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -0.26 (0.57), residues: 169 helix: 0.19 (0.46), residues: 88 sheet: -0.21 (1.31), residues: 19 loop : -0.48 (0.73), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.005 ARG C 461 TYR 0.038 0.007 TYR C 216 PHE 0.020 0.004 PHE C 331 TRP 0.011 0.004 TRP C 345 HIS 0.014 0.005 HIS C 485 Details of bonding type rmsd covalent geometry : bond 0.00988 ( 2270) covalent geometry : angle 1.84631 ( 3215) hydrogen bonds : bond 0.16210 ( 117) hydrogen bonds : angle 7.41123 ( 288) metal coordination : bond 0.03706 ( 4) metal coordination : angle 10.50380 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.061 Fit side-chains REVERT: C 183 ARG cc_start: 0.6513 (mmt180) cc_final: 0.5566 (ptt90) REVERT: C 229 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6855 (pt0) REVERT: C 274 GLN cc_start: 0.7631 (mt0) cc_final: 0.6663 (pm20) REVERT: C 458 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7055 (mmm) REVERT: C 480 GLN cc_start: 0.7885 (pp30) cc_final: 0.7632 (pp30) outliers start: 13 outliers final: 7 residues processed: 54 average time/residue: 0.0687 time to fit residues: 4.2771 Evaluate side-chains 43 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 352 GLN Chi-restraints excluded: chain C residue 458 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 HIS C 480 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.157657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.124334 restraints weight = 3090.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.129145 restraints weight = 1776.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.132549 restraints weight = 1233.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.134804 restraints weight = 960.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.136115 restraints weight = 801.399| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2274 Z= 0.199 Angle : 0.676 8.005 3221 Z= 0.358 Chirality : 0.036 0.127 355 Planarity : 0.004 0.028 286 Dihedral : 27.219 78.497 590 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.67 % Allowed : 14.67 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.64), residues: 169 helix: 2.68 (0.54), residues: 82 sheet: -0.95 (0.76), residues: 33 loop : -0.59 (0.85), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 323 TYR 0.014 0.003 TYR C 216 PHE 0.008 0.002 PHE C 303 TRP 0.011 0.002 TRP C 230 HIS 0.007 0.002 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 2270) covalent geometry : angle 0.64393 ( 3215) hydrogen bonds : bond 0.04533 ( 117) hydrogen bonds : angle 3.42538 ( 288) metal coordination : bond 0.00863 ( 4) metal coordination : angle 4.82539 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.061 Fit side-chains REVERT: C 183 ARG cc_start: 0.6344 (mmt180) cc_final: 0.4978 (ptt90) REVERT: C 216 TYR cc_start: 0.6774 (OUTLIER) cc_final: 0.6436 (t80) REVERT: C 352 GLN cc_start: 0.8485 (mm110) cc_final: 0.8280 (mm110) REVERT: C 355 ASP cc_start: 0.7133 (m-30) cc_final: 0.6850 (m-30) outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.0617 time to fit residues: 2.9233 Evaluate side-chains 36 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 480 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 ASN C 480 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.162056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.129816 restraints weight = 3155.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134535 restraints weight = 1829.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137777 restraints weight = 1282.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.139917 restraints weight = 999.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.141532 restraints weight = 839.287| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2274 Z= 0.186 Angle : 0.611 6.971 3221 Z= 0.332 Chirality : 0.035 0.115 355 Planarity : 0.004 0.028 286 Dihedral : 27.097 59.835 573 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.00 % Allowed : 15.33 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.65), residues: 169 helix: 2.75 (0.55), residues: 82 sheet: -1.52 (0.73), residues: 33 loop : -0.57 (0.86), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 279 TYR 0.014 0.002 TYR C 324 PHE 0.010 0.001 PHE C 464 TRP 0.010 0.002 TRP C 345 HIS 0.007 0.002 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 2270) covalent geometry : angle 0.58424 ( 3215) hydrogen bonds : bond 0.04351 ( 117) hydrogen bonds : angle 3.24738 ( 288) metal coordination : bond 0.00694 ( 4) metal coordination : angle 4.20590 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.068 Fit side-chains REVERT: C 183 ARG cc_start: 0.6276 (mmt180) cc_final: 0.5019 (ptt90) REVERT: C 216 TYR cc_start: 0.6664 (OUTLIER) cc_final: 0.6335 (t80) REVERT: C 274 GLN cc_start: 0.5732 (pm20) cc_final: 0.5473 (pm20) REVERT: C 352 GLN cc_start: 0.8497 (mm110) cc_final: 0.8215 (mm110) REVERT: C 355 ASP cc_start: 0.7272 (m-30) cc_final: 0.7034 (m-30) outliers start: 6 outliers final: 1 residues processed: 36 average time/residue: 0.0775 time to fit residues: 3.1838 Evaluate side-chains 33 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.161836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129832 restraints weight = 3154.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134386 restraints weight = 1801.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137600 restraints weight = 1268.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139898 restraints weight = 991.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.141116 restraints weight = 826.863| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2274 Z= 0.178 Angle : 0.583 5.638 3221 Z= 0.322 Chirality : 0.034 0.143 355 Planarity : 0.004 0.029 286 Dihedral : 26.838 59.182 573 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.67 % Allowed : 15.33 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.66), residues: 169 helix: 2.72 (0.56), residues: 82 sheet: -1.55 (0.81), residues: 26 loop : -0.03 (0.85), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 279 TYR 0.013 0.002 TYR C 188 PHE 0.009 0.001 PHE C 464 TRP 0.011 0.002 TRP C 345 HIS 0.007 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 2270) covalent geometry : angle 0.56349 ( 3215) hydrogen bonds : bond 0.04037 ( 117) hydrogen bonds : angle 3.08277 ( 288) metal coordination : bond 0.00623 ( 4) metal coordination : angle 3.46678 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.065 Fit side-chains REVERT: C 183 ARG cc_start: 0.6244 (mmt180) cc_final: 0.5086 (ptt90) REVERT: C 216 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.6465 (t80) REVERT: C 342 MET cc_start: 0.8092 (ttp) cc_final: 0.7885 (ttp) REVERT: C 352 GLN cc_start: 0.8449 (mm110) cc_final: 0.8233 (mm110) REVERT: C 355 ASP cc_start: 0.7316 (m-30) cc_final: 0.7077 (m-30) outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 0.0729 time to fit residues: 3.2220 Evaluate side-chains 37 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.163641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.130981 restraints weight = 3178.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135761 restraints weight = 1778.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.139090 restraints weight = 1230.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.140979 restraints weight = 953.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142735 restraints weight = 810.222| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2274 Z= 0.178 Angle : 0.567 5.642 3221 Z= 0.315 Chirality : 0.033 0.113 355 Planarity : 0.003 0.030 286 Dihedral : 26.726 59.852 573 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.59 % Allowed : 2.96 % Favored : 96.45 % Rotamer: Outliers : 4.00 % Allowed : 17.33 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.67), residues: 169 helix: 2.73 (0.57), residues: 82 sheet: -1.63 (0.84), residues: 26 loop : 0.11 (0.87), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 279 TYR 0.008 0.001 TYR C 324 PHE 0.008 0.001 PHE C 464 TRP 0.010 0.002 TRP C 345 HIS 0.006 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 2270) covalent geometry : angle 0.54950 ( 3215) hydrogen bonds : bond 0.04067 ( 117) hydrogen bonds : angle 3.08128 ( 288) metal coordination : bond 0.00688 ( 4) metal coordination : angle 3.30814 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.067 Fit side-chains REVERT: C 183 ARG cc_start: 0.6247 (mmt180) cc_final: 0.5212 (ptt90) REVERT: C 216 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6489 (t80) REVERT: C 352 GLN cc_start: 0.8458 (mm110) cc_final: 0.8234 (mm110) outliers start: 6 outliers final: 2 residues processed: 38 average time/residue: 0.0793 time to fit residues: 3.4367 Evaluate side-chains 35 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.163624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.131842 restraints weight = 3170.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.136644 restraints weight = 1814.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139828 restraints weight = 1263.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.141992 restraints weight = 987.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.143529 restraints weight = 825.857| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2274 Z= 0.168 Angle : 0.565 4.704 3221 Z= 0.317 Chirality : 0.034 0.133 355 Planarity : 0.004 0.032 286 Dihedral : 26.635 59.093 573 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.33 % Allowed : 19.33 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.67), residues: 169 helix: 2.91 (0.57), residues: 81 sheet: -1.80 (0.81), residues: 26 loop : 0.20 (0.86), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 461 TYR 0.008 0.001 TYR C 324 PHE 0.008 0.001 PHE C 464 TRP 0.011 0.001 TRP C 345 HIS 0.006 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 2270) covalent geometry : angle 0.55408 ( 3215) hydrogen bonds : bond 0.03921 ( 117) hydrogen bonds : angle 3.05278 ( 288) metal coordination : bond 0.00590 ( 4) metal coordination : angle 2.66118 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.064 Fit side-chains REVERT: C 183 ARG cc_start: 0.6211 (mmt180) cc_final: 0.5216 (ptt90) REVERT: C 216 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.6489 (t80) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.0649 time to fit residues: 2.6525 Evaluate side-chains 33 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.0570 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.164182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133088 restraints weight = 3128.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137766 restraints weight = 1759.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.140848 restraints weight = 1220.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.143056 restraints weight = 953.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.144204 restraints weight = 798.834| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2274 Z= 0.160 Angle : 0.554 4.655 3221 Z= 0.313 Chirality : 0.033 0.130 355 Planarity : 0.003 0.029 286 Dihedral : 26.500 59.632 571 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.59 % Allowed : 2.37 % Favored : 97.04 % Rotamer: Outliers : 2.00 % Allowed : 19.33 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.68), residues: 169 helix: 2.99 (0.58), residues: 81 sheet: -1.85 (0.80), residues: 26 loop : 0.23 (0.86), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 461 TYR 0.013 0.002 TYR C 188 PHE 0.008 0.001 PHE C 464 TRP 0.012 0.001 TRP C 345 HIS 0.005 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2270) covalent geometry : angle 0.54389 ( 3215) hydrogen bonds : bond 0.03758 ( 117) hydrogen bonds : angle 2.97341 ( 288) metal coordination : bond 0.00536 ( 4) metal coordination : angle 2.45515 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: C 183 ARG cc_start: 0.6297 (mmt180) cc_final: 0.5208 (ptt90) REVERT: C 188 TYR cc_start: 0.8154 (t80) cc_final: 0.7657 (t80) REVERT: C 216 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6530 (t80) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.0611 time to fit residues: 2.6719 Evaluate side-chains 38 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 486 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.162657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130525 restraints weight = 3120.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135262 restraints weight = 1726.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.138117 restraints weight = 1190.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.140525 restraints weight = 939.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.141559 restraints weight = 786.156| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2274 Z= 0.193 Angle : 0.578 5.367 3221 Z= 0.324 Chirality : 0.034 0.117 355 Planarity : 0.004 0.030 286 Dihedral : 26.744 59.853 571 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.00 % Allowed : 20.00 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.68), residues: 169 helix: 2.84 (0.58), residues: 81 sheet: -1.88 (0.83), residues: 26 loop : 0.25 (0.86), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 461 TYR 0.012 0.002 TYR C 188 PHE 0.008 0.001 PHE C 464 TRP 0.011 0.001 TRP C 345 HIS 0.005 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 2270) covalent geometry : angle 0.56457 ( 3215) hydrogen bonds : bond 0.04217 ( 117) hydrogen bonds : angle 3.08302 ( 288) metal coordination : bond 0.00788 ( 4) metal coordination : angle 2.88740 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.066 Fit side-chains REVERT: C 183 ARG cc_start: 0.6342 (mmt180) cc_final: 0.5271 (ptt90) REVERT: C 188 TYR cc_start: 0.8136 (t80) cc_final: 0.7652 (t80) REVERT: C 216 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6695 (t80) REVERT: C 352 GLN cc_start: 0.8421 (mm110) cc_final: 0.8178 (mm110) outliers start: 3 outliers final: 1 residues processed: 36 average time/residue: 0.0632 time to fit residues: 2.6727 Evaluate side-chains 36 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 353 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 0.0670 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.162212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130829 restraints weight = 3178.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135458 restraints weight = 1777.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138608 restraints weight = 1231.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.140479 restraints weight = 962.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.142186 restraints weight = 814.714| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2274 Z= 0.181 Angle : 0.577 4.772 3221 Z= 0.325 Chirality : 0.034 0.128 355 Planarity : 0.004 0.029 286 Dihedral : 26.654 59.946 571 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.00 % Allowed : 19.33 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.69), residues: 169 helix: 2.94 (0.58), residues: 81 sheet: -1.81 (0.86), residues: 26 loop : 0.35 (0.88), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 461 TYR 0.012 0.002 TYR C 188 PHE 0.008 0.001 PHE C 464 TRP 0.011 0.001 TRP C 345 HIS 0.005 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 2270) covalent geometry : angle 0.56649 ( 3215) hydrogen bonds : bond 0.04004 ( 117) hydrogen bonds : angle 3.05526 ( 288) metal coordination : bond 0.00693 ( 4) metal coordination : angle 2.59111 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.043 Fit side-chains REVERT: C 183 ARG cc_start: 0.6362 (mmt180) cc_final: 0.5222 (ptt90) REVERT: C 188 TYR cc_start: 0.8156 (t80) cc_final: 0.7682 (t80) REVERT: C 216 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.6677 (t80) REVERT: C 352 GLN cc_start: 0.8418 (mm110) cc_final: 0.8123 (mm110) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.0559 time to fit residues: 2.4137 Evaluate side-chains 37 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 353 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.163435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.133089 restraints weight = 3141.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137578 restraints weight = 1660.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140632 restraints weight = 1119.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142784 restraints weight = 861.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144227 restraints weight = 713.228| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2274 Z= 0.179 Angle : 0.573 5.239 3221 Z= 0.322 Chirality : 0.034 0.128 355 Planarity : 0.003 0.029 286 Dihedral : 26.600 59.995 571 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.00 % Allowed : 19.33 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.68), residues: 169 helix: 2.91 (0.57), residues: 81 sheet: -1.77 (0.87), residues: 26 loop : 0.33 (0.87), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 461 TYR 0.012 0.002 TYR C 188 PHE 0.008 0.001 PHE C 464 TRP 0.012 0.002 TRP C 345 HIS 0.005 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 2270) covalent geometry : angle 0.56417 ( 3215) hydrogen bonds : bond 0.03900 ( 117) hydrogen bonds : angle 2.99155 ( 288) metal coordination : bond 0.00659 ( 4) metal coordination : angle 2.42072 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 338 Ramachandran restraints generated. 169 Oldfield, 0 Emsley, 169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.067 Fit side-chains REVERT: C 183 ARG cc_start: 0.6429 (mmt180) cc_final: 0.5167 (ptt90) REVERT: C 188 TYR cc_start: 0.8203 (t80) cc_final: 0.7698 (t80) REVERT: C 216 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.6620 (t80) REVERT: C 352 GLN cc_start: 0.8588 (mm110) cc_final: 0.8344 (mm110) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.0661 time to fit residues: 2.8778 Evaluate side-chains 36 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 TYR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 473 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 7 optimal weight: 0.3980 chunk 5 optimal weight: 0.0270 chunk 13 optimal weight: 0.8980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.164750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.133667 restraints weight = 3241.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.138402 restraints weight = 1777.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.141447 restraints weight = 1221.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.143703 restraints weight = 948.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.145035 restraints weight = 795.241| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2274 Z= 0.158 Angle : 0.553 5.342 3221 Z= 0.314 Chirality : 0.032 0.109 355 Planarity : 0.003 0.029 286 Dihedral : 26.401 59.839 571 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.33 % Allowed : 20.67 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.68), residues: 169 helix: 2.90 (0.56), residues: 81 sheet: -1.73 (0.87), residues: 26 loop : 0.36 (0.88), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 461 TYR 0.012 0.002 TYR C 188 PHE 0.008 0.001 PHE C 464 TRP 0.013 0.001 TRP C 345 HIS 0.005 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 2270) covalent geometry : angle 0.54568 ( 3215) hydrogen bonds : bond 0.03541 ( 117) hydrogen bonds : angle 2.92547 ( 288) metal coordination : bond 0.00507 ( 4) metal coordination : angle 2.12710 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 665.33 seconds wall clock time: 11 minutes 58.58 seconds (718.58 seconds total)