Starting phenix.real_space_refine on Tue Aug 4 14:05:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu8_60893/08_2026/9iu8_60893.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu8_60893/08_2026/9iu8_60893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iu8_60893/08_2026/9iu8_60893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu8_60893/08_2026/9iu8_60893.map" model { file = "/net/cci-nas-00/data/ceres_data/9iu8_60893/08_2026/9iu8_60893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu8_60893/08_2026/9iu8_60893.cif" } resolution = 3.21 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= 0.037 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 50 5.49 5 S 10 5.16 5 C 2087 2.51 5 N 665 2.21 5 O 769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 3582 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2556 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain breaks: 2 Chain: "E" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" 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 1299 SG CYS A 304 39.237 71.171 21.241 1.00229.33 S ATOM 1317 SG CYS A 307 39.849 68.304 19.028 1.00230.02 S ATOM 1468 SG CYS A 326 42.252 69.065 21.275 1.00223.79 S ATOM 1540 SG CYS A 335 41.923 71.881 18.609 1.00234.93 S Time building chain proxies: 0.99, per 1000 atoms: 0.28 Number of scatterers: 3582 At special positions: 0 Unit cell: (74.0773, 101.121, 63.4948, 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 10 16.00 P 50 15.00 O 769 8.00 N 665 7.00 C 2087 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: 0.20 Conformation dependent library (CDL) restraints added in 59.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 304 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 307 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 326 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 335 " Number of angles added : 6 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 588 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 5 sheets defined 49.5% alpha, 13.5% beta 25 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.631A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 209 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 271 through 283 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 342 through 358 Processing helix chain 'A' and resid 371 through 388 removed outlier: 3.743A pdb=" N VAL A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 423 removed outlier: 3.679A pdb=" N LEU A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.782A pdb=" N GLU A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 459 Processing helix chain 'A' and resid 478 through 486 Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166 Processing sheet with id=AA2, first strand: chain 'A' and resid 249 through 250 Processing sheet with id=AA3, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 315 Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 368 removed outlier: 5.184A pdb=" N GLN A 437 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N GLU A 364 " --> pdb=" O THR A 435 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A 435 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 366 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG A 433 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 368 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU A 431 " --> pdb=" O VAL A 368 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 0.46 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 686 1.34 - 1.46: 1213 1.46 - 1.57: 1750 1.57 - 1.69: 98 1.69 - 1.81: 15 Bond restraints: 3762 Sorted by residual: bond pdb=" N1 DC F 30 " pdb=" C6 DC F 30 " ideal model delta sigma weight residual 1.367 1.331 0.036 6.00e-03 2.78e+04 3.68e+01 bond pdb=" C4 DC F 30 " pdb=" C5 DC F 30 " ideal model delta sigma weight residual 1.425 1.402 0.023 8.00e-03 1.56e+04 8.30e+00 bond pdb=" N1 DC E 21 " pdb=" C6 DC E 21 " ideal model delta sigma weight residual 1.367 1.350 0.017 6.00e-03 2.78e+04 8.14e+00 bond pdb=" P DG E 1 " pdb=" O5' DG E 1 " ideal model delta sigma weight residual 1.593 1.621 -0.028 1.00e-02 1.00e+04 8.00e+00 bond pdb=" C LYS A 289 " pdb=" N PRO A 290 " ideal model delta sigma weight residual 1.329 1.362 -0.034 1.20e-02 6.94e+03 7.87e+00 ... (remaining 3757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 4772 2.63 - 5.27: 496 5.27 - 7.90: 33 7.90 - 10.53: 3 10.53 - 13.17: 2 Bond angle restraints: 5306 Sorted by residual: angle pdb=" O3' DG F 32 " pdb=" P DT F 33 " pdb=" O5' DT F 33 " ideal model delta sigma weight residual 104.00 90.83 13.17 1.90e+00 2.77e-01 4.80e+01 angle pdb=" N ARG A 155 " pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " ideal model delta sigma weight residual 110.46 120.73 -10.27 1.57e+00 4.06e-01 4.28e+01 angle pdb=" O4' DG F 31 " pdb=" C1' DG F 31 " pdb=" C2' DG F 31 " ideal model delta sigma weight residual 105.90 100.89 5.01 8.00e-01 1.56e+00 3.92e+01 angle pdb=" C ARG A 155 " pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " ideal model delta sigma weight residual 109.72 98.91 10.81 1.92e+00 2.71e-01 3.17e+01 angle pdb=" O4' DT F 33 " pdb=" C1' DT F 33 " pdb=" N1 DT F 33 " ideal model delta sigma weight residual 108.00 111.83 -3.83 7.00e-01 2.04e+00 3.00e+01 ... (remaining 5301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 1605 16.02 - 32.05: 255 32.05 - 48.07: 130 48.07 - 64.09: 98 64.09 - 80.12: 12 Dihedral angle restraints: 2100 sinusoidal: 1188 harmonic: 912 Sorted by residual: dihedral pdb=" CA ARG A 155 " pdb=" C ARG A 155 " pdb=" N GLY A 156 " pdb=" CA GLY A 156 " ideal model delta harmonic sigma weight residual -180.00 -159.20 -20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PRO A 197 " pdb=" C PRO A 197 " pdb=" N LEU A 198 " pdb=" CA LEU A 198 " ideal model delta harmonic sigma weight residual -180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C ARG A 155 " pdb=" N ARG A 155 " pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " ideal model delta harmonic sigma weight residual -122.60 -113.31 -9.29 0 2.50e+00 1.60e-01 1.38e+01 ... (remaining 2097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 508 0.130 - 0.260: 60 0.260 - 0.391: 2 0.391 - 0.521: 1 0.521 - 0.651: 2 Chirality restraints: 573 Sorted by residual: chirality pdb=" P DC F 28 " pdb=" OP1 DC F 28 " pdb=" OP2 DC F 28 " pdb=" O5' DC F 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P DG E 1 " pdb=" OP1 DG E 1 " pdb=" OP2 DG E 1 " pdb=" O5' DG E 1 " both_signs ideal model delta sigma weight residual True 2.34 2.96 -0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" P DG F 31 " pdb=" OP1 DG F 31 " pdb=" OP2 DG F 31 " pdb=" O5' DG F 31 " both_signs ideal model delta sigma weight residual True 2.34 -2.74 -0.41 2.00e-01 2.50e+01 4.16e+00 ... (remaining 570 not shown) Planarity restraints: 516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 237 " 0.349 9.50e-02 1.11e+02 1.57e-01 1.75e+01 pdb=" NE ARG A 237 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 237 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 237 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 237 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 173 " 0.297 9.50e-02 1.11e+02 1.34e-01 1.32e+01 pdb=" NE ARG A 173 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 173 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 173 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 173 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG F 35 " -0.042 2.00e-02 2.50e+03 1.81e-02 9.86e+00 pdb=" N9 DG F 35 " 0.041 2.00e-02 2.50e+03 pdb=" C8 DG F 35 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG F 35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG F 35 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG F 35 " -0.009 2.00e-02 2.50e+03 pdb=" O6 DG F 35 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG F 35 " -0.006 2.00e-02 2.50e+03 pdb=" C2 DG F 35 " -0.006 2.00e-02 2.50e+03 pdb=" N2 DG F 35 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG F 35 " 0.016 2.00e-02 2.50e+03 pdb=" C4 DG F 35 " 0.008 2.00e-02 2.50e+03 ... (remaining 513 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 585 2.81 - 3.33: 3165 3.33 - 3.85: 6633 3.85 - 4.38: 7511 4.38 - 4.90: 11492 Nonbonded interactions: 29386 Sorted by model distance: nonbonded pdb=" OG SER A 157 " pdb=" O2 DC E 22 " model vdw 2.283 3.040 nonbonded pdb=" OG SER A 212 " pdb=" OP1 DG F 35 " model vdw 2.396 3.040 nonbonded pdb=" NH1 ARG A 183 " pdb=" OE1 GLU A 186 " model vdw 2.459 3.120 nonbonded pdb=" O4' DC E 22 " pdb=" O2 DC E 22 " model vdw 2.499 3.040 nonbonded pdb=" O5' DG F 34 " pdb=" O4' DG F 34 " model vdw 2.526 2.432 ... (remaining 29381 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: 1.120 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: 5.560 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5360 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 : 0.009 0.049 3766 Z= 0.628 Angle : 1.655 16.813 5312 Z= 1.103 Chirality : 0.091 0.651 573 Planarity : 0.018 0.157 516 Dihedral : 22.314 80.118 1512 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.26 % Allowed : 4.53 % Favored : 93.21 % Cbeta Deviations : 0.34 % 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: -1.91 (0.40), residues: 313 helix: -1.25 (0.36), residues: 136 sheet: -1.33 (0.75), residues: 37 loop : -1.09 (0.46), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.005 ARG A 237 TYR 0.020 0.005 TYR A 312 PHE 0.024 0.003 PHE A 217 TRP 0.015 0.002 TRP A 161 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00948 / 0.63 ( 3762) covalent geometry : angle 1.62077 / 1.10 ( 5306) hydrogen bonds : bond 0.17419 / 12.02 ( 185) hydrogen bonds : angle 6.90061 / 5.19 ( 466) metal coordination : bond 0.01390 / 0.73 ( 4) metal coordination : angle 10.04885 / 7.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.104 Fit side-chains REVERT: A 155 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6107 (ttp-110) REVERT: A 272 ARG cc_start: 0.5015 (ttp-110) cc_final: 0.4472 (ttm-80) REVERT: A 294 THR cc_start: 0.7699 (m) cc_final: 0.7468 (p) REVERT: A 324 TYR cc_start: 0.5490 (m-80) cc_final: 0.5237 (m-80) REVERT: A 371 SER cc_start: 0.6115 (t) cc_final: 0.5804 (m) REVERT: A 420 LEU cc_start: 0.5522 (mt) cc_final: 0.5319 (mt) REVERT: A 434 GLU cc_start: 0.7869 (mt-10) cc_final: 0.6820 (mm-30) REVERT: A 474 ILE cc_start: 0.7350 (mp) cc_final: 0.7136 (mp) outliers start: 6 outliers final: 2 residues processed: 47 average time/residue: 0.1226 time to fit residues: 6.5058 Evaluate side-chains 31 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 463 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.210966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150935 restraints weight = 4047.068| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.01 r_work: 0.3360 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 3766 Z= 0.402 Angle : 0.889 10.391 5312 Z= 0.478 Chirality : 0.053 0.235 573 Planarity : 0.008 0.062 516 Dihedral : 25.761 89.184 897 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.02 % Allowed : 7.55 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.46), residues: 313 helix: 0.82 (0.43), residues: 138 sheet: -1.43 (0.57), residues: 65 loop : -0.53 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 237 TYR 0.025 0.004 TYR A 482 PHE 0.012 0.003 PHE A 464 TRP 0.013 0.002 TRP A 442 HIS 0.009 0.002 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00865 / 0.40 ( 3762) covalent geometry : angle 0.87286 / 0.48 ( 5306) hydrogen bonds : bond 0.06764 / 4.36 ( 185) hydrogen bonds : angle 4.41224 / 3.50 ( 466) metal coordination : bond 0.01101 / 0.55 ( 4) metal coordination : angle 5.01794 / 4.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.111 Fit side-chains REVERT: A 155 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7753 (ptt90) REVERT: A 226 GLN cc_start: 0.7602 (mp10) cc_final: 0.7086 (mp10) REVERT: A 272 ARG cc_start: 0.8456 (ttp-110) cc_final: 0.7479 (ttm-80) REVERT: A 371 SER cc_start: 0.7703 (t) cc_final: 0.7227 (m) outliers start: 8 outliers final: 7 residues processed: 31 average time/residue: 0.0893 time to fit residues: 3.3858 Evaluate side-chains 28 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 463 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.223720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.164209 restraints weight = 3904.230| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.12 r_work: 0.3454 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3766 Z= 0.169 Angle : 0.650 8.864 5312 Z= 0.370 Chirality : 0.042 0.226 573 Planarity : 0.005 0.036 516 Dihedral : 25.898 86.419 897 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.26 % Allowed : 11.32 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.47), residues: 313 helix: 1.66 (0.43), residues: 140 sheet: -0.98 (0.59), residues: 63 loop : -0.04 (0.60), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 223 TYR 0.018 0.002 TYR A 482 PHE 0.008 0.002 PHE A 314 TRP 0.012 0.001 TRP A 442 HIS 0.003 0.001 HIS A 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 ( 3762) covalent geometry : angle 0.63910 / 0.37 ( 5306) hydrogen bonds : bond 0.04670 / 3.12 ( 185) hydrogen bonds : angle 3.95097 / 3.19 ( 466) metal coordination : bond 0.01114 / 0.56 ( 4) metal coordination : angle 3.56376 / 3.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.117 Fit side-chains REVERT: A 155 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7634 (ptt90) REVERT: A 226 GLN cc_start: 0.7688 (mp10) cc_final: 0.7352 (mp10) REVERT: A 272 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.7287 (ttm-80) REVERT: A 371 SER cc_start: 0.7568 (t) cc_final: 0.7025 (m) REVERT: A 434 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7595 (mm-30) REVERT: A 463 THR cc_start: 0.7722 (OUTLIER) cc_final: 0.7434 (t) outliers start: 6 outliers final: 3 residues processed: 30 average time/residue: 0.0823 time to fit residues: 3.0880 Evaluate side-chains 28 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 463 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.4342 r_free = 0.4342 target = 0.211797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152356 restraints weight = 3914.118| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.82 r_work: 0.3455 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3766 Z= 0.256 Angle : 0.695 9.317 5312 Z= 0.383 Chirality : 0.043 0.258 573 Planarity : 0.005 0.042 516 Dihedral : 26.190 88.271 897 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.64 % Allowed : 11.70 % Favored : 85.66 % 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: 0.90 (0.47), residues: 313 helix: 1.81 (0.43), residues: 140 sheet: -1.10 (0.61), residues: 61 loop : 0.21 (0.60), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 416 TYR 0.016 0.003 TYR A 482 PHE 0.012 0.002 PHE A 464 TRP 0.012 0.002 TRP A 442 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.26 ( 3762) covalent geometry : angle 0.68563 / 0.38 ( 5306) hydrogen bonds : bond 0.05079 / 3.29 ( 185) hydrogen bonds : angle 3.99346 / 3.21 ( 466) metal coordination : bond 0.01173 / 0.59 ( 4) metal coordination : angle 3.36715 / 2.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.108 Fit side-chains REVERT: A 155 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7817 (ptt90) REVERT: A 177 ASP cc_start: 0.8291 (t0) cc_final: 0.8068 (t0) REVERT: A 226 GLN cc_start: 0.7564 (mp10) cc_final: 0.7176 (mp10) REVERT: A 272 ARG cc_start: 0.8368 (ttp-110) cc_final: 0.7325 (ttm-80) REVERT: A 371 SER cc_start: 0.7633 (t) cc_final: 0.7149 (m) REVERT: A 434 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7670 (mm-30) REVERT: A 463 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7402 (t) outliers start: 7 outliers final: 5 residues processed: 32 average time/residue: 0.0906 time to fit residues: 3.5214 Evaluate side-chains 33 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 463 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4446 r_free = 0.4446 target = 0.223115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.156617 restraints weight = 3940.798| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.11 r_work: 0.3450 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3766 Z= 0.172 Angle : 0.624 9.873 5312 Z= 0.352 Chirality : 0.041 0.245 573 Planarity : 0.004 0.034 516 Dihedral : 26.065 87.024 897 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.02 % Allowed : 10.57 % Favored : 86.42 % 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: 1.26 (0.48), residues: 313 helix: 2.08 (0.43), residues: 140 sheet: -1.11 (0.65), residues: 51 loop : 0.39 (0.57), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.016 0.002 TYR A 154 PHE 0.009 0.002 PHE A 314 TRP 0.012 0.001 TRP A 345 HIS 0.002 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 ( 3762) covalent geometry : angle 0.61737 / 0.35 ( 5306) hydrogen bonds : bond 0.04226 / 2.78 ( 185) hydrogen bonds : angle 3.90187 / 3.15 ( 466) metal coordination : bond 0.00738 / 0.37 ( 4) metal coordination : angle 2.75990 / 2.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.115 Fit side-chains REVERT: A 155 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7616 (ttp80) REVERT: A 226 GLN cc_start: 0.7612 (mp10) cc_final: 0.7338 (mp10) REVERT: A 272 ARG cc_start: 0.8272 (ttp-110) cc_final: 0.7328 (ttm-80) REVERT: A 283 VAL cc_start: 0.7779 (OUTLIER) cc_final: 0.7516 (t) REVERT: A 371 SER cc_start: 0.7593 (t) cc_final: 0.7109 (m) REVERT: A 434 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7732 (mm-30) REVERT: A 463 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7372 (t) outliers start: 8 outliers final: 3 residues processed: 32 average time/residue: 0.0954 time to fit residues: 3.6919 Evaluate side-chains 28 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 463 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.0000 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 = 0.4445 r_free = 0.4445 target = 0.222777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.162208 restraints weight = 3957.781| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.85 r_work: 0.3450 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3766 Z= 0.177 Angle : 0.616 10.651 5312 Z= 0.345 Chirality : 0.040 0.242 573 Planarity : 0.004 0.033 516 Dihedral : 26.077 86.891 897 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.15 % Allowed : 9.06 % Favored : 86.79 % 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: 1.54 (0.48), residues: 313 helix: 2.29 (0.43), residues: 141 sheet: -0.97 (0.67), residues: 51 loop : 0.56 (0.59), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 444 TYR 0.015 0.002 TYR A 154 PHE 0.010 0.002 PHE A 464 TRP 0.011 0.001 TRP A 345 HIS 0.002 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 ( 3762) covalent geometry : angle 0.60986 / 0.35 ( 5306) hydrogen bonds : bond 0.04196 / 2.70 ( 185) hydrogen bonds : angle 3.77588 / 3.05 ( 466) metal coordination : bond 0.00764 / 0.38 ( 4) metal coordination : angle 2.59370 / 2.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.143 Fit side-chains REVERT: A 155 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7504 (ptt90) REVERT: A 226 GLN cc_start: 0.7690 (mp10) cc_final: 0.7416 (mp10) REVERT: A 272 ARG cc_start: 0.8329 (ttp-110) cc_final: 0.7365 (ttm-80) REVERT: A 283 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7535 (t) REVERT: A 371 SER cc_start: 0.7581 (t) cc_final: 0.7054 (m) REVERT: A 463 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7564 (t) outliers start: 11 outliers final: 6 residues processed: 33 average time/residue: 0.0943 time to fit residues: 3.7704 Evaluate side-chains 31 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 463 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.0970 chunk 24 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 0.0050 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 HIS A 334 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.225360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.165340 restraints weight = 4031.538| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.16 r_work: 0.3476 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3766 Z= 0.138 Angle : 0.574 11.579 5312 Z= 0.325 Chirality : 0.038 0.220 573 Planarity : 0.004 0.030 516 Dihedral : 25.972 86.392 897 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.64 % Allowed : 10.94 % Favored : 86.42 % 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: 1.88 (0.48), residues: 313 helix: 2.61 (0.43), residues: 141 sheet: -0.79 (0.68), residues: 49 loop : 0.65 (0.59), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.014 0.002 TYR A 154 PHE 0.008 0.001 PHE A 314 TRP 0.012 0.001 TRP A 345 HIS 0.008 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 ( 3762) covalent geometry : angle 0.57006 / 0.32 ( 5306) hydrogen bonds : bond 0.03677 / 2.40 ( 185) hydrogen bonds : angle 3.71824 / 3.01 ( 466) metal coordination : bond 0.00537 / 0.27 ( 4) metal coordination : angle 2.09013 / 1.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.107 Fit side-chains REVERT: A 155 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7294 (ttp80) REVERT: A 226 GLN cc_start: 0.7683 (mp10) cc_final: 0.7478 (mp10) REVERT: A 272 ARG cc_start: 0.8288 (ttp-110) cc_final: 0.7396 (ttm-80) REVERT: A 371 SER cc_start: 0.7532 (t) cc_final: 0.7032 (m) REVERT: A 434 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7635 (mm-30) outliers start: 7 outliers final: 4 residues processed: 31 average time/residue: 0.0846 time to fit residues: 3.1805 Evaluate side-chains 29 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 460 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4461 r_free = 0.4461 target = 0.224492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.165496 restraints weight = 3998.927| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.92 r_work: 0.3500 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3766 Z= 0.158 Angle : 0.585 11.551 5312 Z= 0.328 Chirality : 0.038 0.233 573 Planarity : 0.004 0.029 516 Dihedral : 25.966 86.341 895 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.89 % Allowed : 10.94 % Favored : 87.17 % 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: 1.92 (0.48), residues: 313 helix: 2.61 (0.43), residues: 141 sheet: -0.73 (0.68), residues: 49 loop : 0.69 (0.59), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.012 0.002 TYR A 154 PHE 0.011 0.002 PHE A 464 TRP 0.010 0.001 TRP A 345 HIS 0.002 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 ( 3762) covalent geometry : angle 0.58134 / 0.33 ( 5306) hydrogen bonds : bond 0.03812 / 2.46 ( 185) hydrogen bonds : angle 3.71838 / 3.00 ( 466) metal coordination : bond 0.00625 / 0.31 ( 4) metal coordination : angle 2.12509 / 1.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.064 Fit side-chains REVERT: A 155 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7445 (ptm-80) REVERT: A 226 GLN cc_start: 0.7685 (mp10) cc_final: 0.7484 (mp10) REVERT: A 272 ARG cc_start: 0.8305 (ttp-110) cc_final: 0.7402 (ttm-80) REVERT: A 371 SER cc_start: 0.7538 (t) cc_final: 0.7043 (m) outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.0597 time to fit residues: 2.0368 Evaluate side-chains 29 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 460 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4438 r_free = 0.4438 target = 0.222062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.185943 restraints weight = 3953.452| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.08 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3766 Z= 0.231 Angle : 0.652 12.023 5312 Z= 0.355 Chirality : 0.041 0.251 573 Planarity : 0.005 0.033 516 Dihedral : 26.115 88.575 895 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.26 % Allowed : 10.94 % Favored : 86.79 % 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: 1.73 (0.48), residues: 313 helix: 2.26 (0.43), residues: 144 sheet: -0.93 (0.67), residues: 49 loop : 0.86 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 416 TYR 0.015 0.002 TYR A 154 PHE 0.012 0.002 PHE A 464 TRP 0.008 0.001 TRP A 345 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.23 ( 3762) covalent geometry : angle 0.64694 / 0.36 ( 5306) hydrogen bonds : bond 0.04355 / 2.81 ( 185) hydrogen bonds : angle 3.80107 / 3.06 ( 466) metal coordination : bond 0.00888 / 0.45 ( 4) metal coordination : angle 2.53386 / 1.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.109 Fit side-chains REVERT: A 155 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7513 (ttp80) REVERT: A 226 GLN cc_start: 0.7686 (mp10) cc_final: 0.7474 (mp10) REVERT: A 272 ARG cc_start: 0.7889 (ttp-110) cc_final: 0.7469 (ttm-80) REVERT: A 283 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7611 (t) outliers start: 6 outliers final: 4 residues processed: 29 average time/residue: 0.0982 time to fit residues: 3.4353 Evaluate side-chains 29 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 34 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 8 optimal weight: 0.0470 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- 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 = 0.4440 r_free = 0.4440 target = 0.222308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.185976 restraints weight = 3993.824| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.03 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3766 Z= 0.207 Angle : 0.639 12.904 5312 Z= 0.349 Chirality : 0.040 0.240 573 Planarity : 0.004 0.031 516 Dihedral : 26.125 88.502 895 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.26 % Allowed : 11.32 % Favored : 86.42 % 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: 1.82 (0.48), residues: 313 helix: 2.48 (0.43), residues: 141 sheet: -0.77 (0.67), residues: 51 loop : 0.74 (0.60), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 223 TYR 0.015 0.002 TYR A 154 PHE 0.011 0.002 PHE A 464 TRP 0.010 0.001 TRP A 345 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.21 ( 3762) covalent geometry : angle 0.63378 / 0.35 ( 5306) hydrogen bonds : bond 0.04175 / 2.70 ( 185) hydrogen bonds : angle 3.80337 / 3.06 ( 466) metal coordination : bond 0.00833 / 0.42 ( 4) metal coordination : angle 2.50812 / 1.93 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.065 Fit side-chains REVERT: A 155 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7312 (ptt90) REVERT: A 272 ARG cc_start: 0.7774 (ttp-110) cc_final: 0.7324 (ttm-80) REVERT: A 283 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7634 (t) outliers start: 6 outliers final: 4 residues processed: 29 average time/residue: 0.0996 time to fit residues: 3.4204 Evaluate side-chains 28 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.0270 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 0.0870 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.225445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.166427 restraints weight = 3938.588| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.15 r_work: 0.3522 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3766 Z= 0.131 Angle : 0.578 13.062 5312 Z= 0.324 Chirality : 0.037 0.215 573 Planarity : 0.004 0.029 516 Dihedral : 25.881 88.462 895 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.89 % Allowed : 12.08 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.49), residues: 313 helix: 2.76 (0.44), residues: 141 sheet: -0.68 (0.67), residues: 49 loop : 0.88 (0.59), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.010 0.001 TYR A 154 PHE 0.007 0.001 PHE A 314 TRP 0.015 0.001 TRP A 345 HIS 0.002 0.000 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 ( 3762) covalent geometry : angle 0.57403 / 0.32 ( 5306) hydrogen bonds : bond 0.03545 / 2.33 ( 185) hydrogen bonds : angle 3.68940 / 2.97 ( 466) metal coordination : bond 0.00497 / 0.25 ( 4) metal coordination : angle 2.18639 / 1.69 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1116.85 seconds wall clock time: 19 minutes 43.75 seconds (1183.75 seconds total)