Starting phenix.real_space_refine on Wed Aug 5 02:26:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11hu_75703/08_2026/11hu_75703.cif Found real_map, /net/cci-nas-00/data/ceres_data/11hu_75703/08_2026/11hu_75703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11hu_75703/08_2026/11hu_75703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11hu_75703/08_2026/11hu_75703.map" model { file = "/net/cci-nas-00/data/ceres_data/11hu_75703/08_2026/11hu_75703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11hu_75703/08_2026/11hu_75703.cif" } resolution = 2.9 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 192 5.49 5 Mg 2 5.21 5 S 23 5.16 5 C 4327 2.51 5 N 1525 2.21 5 O 2018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8088 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3980 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 21, 'TRANS': 473} Chain: "D" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 179 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 3926 Classifications: {'RNA': 183} Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 13, 'rna3p_pur': 87, 'rna3p_pyr': 63} Link IDs: {'rna2p': 32, 'rna3p': 150} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1879 SG CYS A 234 74.814 15.058 66.994 1.00248.14 S ATOM 1904 SG CYS A 237 78.071 13.701 68.506 1.00248.22 S ATOM 2132 SG CYS A 265 75.485 11.412 66.886 1.00244.98 S Time building chain proxies: 1.61, per 1000 atoms: 0.20 Number of scatterers: 8088 At special positions: 0 Unit cell: (89.1, 116.325, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 23 16.00 P 192 15.00 Mg 2 11.99 O 2018 8.00 N 1525 7.00 C 4327 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: 0.45 Conformation dependent library (CDL) restraints added in 225.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 503 " pdb="ZN ZN A 503 " - pdb=" ND1 HIS A 268 " pdb="ZN ZN A 503 " - pdb=" SG CYS A 234 " pdb="ZN ZN A 503 " - pdb=" SG CYS A 265 " pdb="ZN ZN A 503 " - pdb=" SG CYS A 237 " Number of angles added : 3 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 924 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 6 sheets defined 36.2% alpha, 15.8% beta 64 base pairs and 99 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 88 through 108 removed outlier: 4.466A pdb=" N LYS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 163 through 182 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 275 through 293 Processing helix chain 'A' and resid 302 through 314 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 341 through 350 removed outlier: 3.998A pdb=" N ALA A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 416 Processing helix chain 'A' and resid 417 through 424 removed outlier: 3.521A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.529A pdb=" N GLY A 464 " --> pdb=" O ARG A 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 6.319A pdb=" N TYR A 5 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU A 44 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE A 7 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 208 removed outlier: 6.939A pdb=" N GLN A 207 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N SER A 322 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU A 55 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR A 72 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER A 77 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N TYR A 365 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN A 80 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL A 367 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN A 82 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLN A 369 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLU A 84 " --> pdb=" O GLN A 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 246 Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 393 Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 478 removed outlier: 6.537A pdb=" N VAL A 446 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N TYR A 484 " --> pdb=" O VAL A 446 " (cutoff:3.500A) 160 hydrogen bonds defined for protein. 453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 166 hydrogen bonds 304 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 99 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 0.62 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: 1875 1.34 - 1.46: 2870 1.46 - 1.58: 3492 1.58 - 1.70: 381 1.70 - 1.82: 37 Bond restraints: 8655 Sorted by residual: bond pdb=" N9 A B 34 " pdb=" C4 A B 34 " ideal model delta sigma weight residual 1.374 1.387 -0.013 6.00e-03 2.78e+04 4.76e+00 bond pdb=" C3' DT D 7 " pdb=" O3' DT D 7 " ideal model delta sigma weight residual 1.435 1.410 0.025 1.30e-02 5.92e+03 3.72e+00 bond pdb=" C4' DG D 5 " pdb=" C3' DG D 5 " ideal model delta sigma weight residual 1.529 1.510 0.019 1.00e-02 1.00e+04 3.48e+00 bond pdb=" C4' DT D 3 " pdb=" C3' DT D 3 " ideal model delta sigma weight residual 1.529 1.510 0.019 1.00e-02 1.00e+04 3.46e+00 bond pdb=" C3' DC D 8 " pdb=" O3' DC D 8 " ideal model delta sigma weight residual 1.435 1.412 0.023 1.30e-02 5.92e+03 3.02e+00 ... (remaining 8650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 11847 1.46 - 2.92: 700 2.92 - 4.38: 51 4.38 - 5.83: 5 5.83 - 7.29: 1 Bond angle restraints: 12604 Sorted by residual: angle pdb=" O2 C B 219 " pdb=" C2 C B 219 " pdb=" N3 C B 219 " ideal model delta sigma weight residual 121.90 118.11 3.79 7.00e-01 2.04e+00 2.94e+01 angle pdb=" C1' C B 88 " pdb=" N1 C B 88 " pdb=" C2 C B 88 " ideal model delta sigma weight residual 118.80 124.25 -5.45 1.10e+00 8.26e-01 2.45e+01 angle pdb=" O2 C B 49 " pdb=" C2 C B 49 " pdb=" N3 C B 49 " ideal model delta sigma weight residual 121.90 118.78 3.12 7.00e-01 2.04e+00 1.99e+01 angle pdb=" O5' G B 195 " pdb=" C5' G B 195 " pdb=" C4' G B 195 " ideal model delta sigma weight residual 109.40 112.84 -3.44 8.00e-01 1.56e+00 1.85e+01 angle pdb=" O4' DT D 3 " pdb=" C4' DT D 3 " pdb=" C3' DT D 3 " ideal model delta sigma weight residual 106.00 103.49 2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 12599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 4938 35.73 - 71.47: 410 71.47 - 107.20: 52 107.20 - 142.94: 3 142.94 - 178.67: 6 Dihedral angle restraints: 5409 sinusoidal: 3972 harmonic: 1437 Sorted by residual: dihedral pdb=" O4' C B 49 " pdb=" C1' C B 49 " pdb=" N1 C B 49 " pdb=" C2 C B 49 " ideal model delta sinusoidal sigma weight residual 200.00 47.12 152.88 1 1.50e+01 4.44e-03 8.06e+01 dihedral pdb=" O4' U B 229 " pdb=" C1' U B 229 " pdb=" N1 U B 229 " pdb=" C2 U B 229 " ideal model delta sinusoidal sigma weight residual 232.00 53.33 178.67 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C B 83 " pdb=" C1' C B 83 " pdb=" N1 C B 83 " pdb=" C2 C B 83 " ideal model delta sinusoidal sigma weight residual -128.00 49.79 -177.79 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 5406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1235 0.061 - 0.123: 139 0.123 - 0.184: 152 0.184 - 0.246: 1 0.246 - 0.307: 1 Chirality restraints: 1528 Sorted by residual: chirality pdb=" CB ILE A 145 " pdb=" CA ILE A 145 " pdb=" CG1 ILE A 145 " pdb=" CG2 ILE A 145 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C1' G B 7 " pdb=" O4' G B 7 " pdb=" C2' G B 7 " pdb=" N9 G B 7 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" C3' A B 86 " pdb=" C4' A B 86 " pdb=" O3' A B 86 " pdb=" C2' A B 86 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 1525 not shown) Planarity restraints: 897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 219 " 0.008 2.00e-02 2.50e+03 1.96e-02 8.64e+00 pdb=" N1 C B 219 " -0.005 2.00e-02 2.50e+03 pdb=" C2 C B 219 " -0.049 2.00e-02 2.50e+03 pdb=" O2 C B 219 " 0.026 2.00e-02 2.50e+03 pdb=" N3 C B 219 " 0.009 2.00e-02 2.50e+03 pdb=" C4 C B 219 " -0.010 2.00e-02 2.50e+03 pdb=" N4 C B 219 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C B 219 " 0.005 2.00e-02 2.50e+03 pdb=" C6 C B 219 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 163 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO A 164 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 80 " 0.028 2.00e-02 2.50e+03 1.22e-02 4.44e+00 pdb=" N9 G B 80 " -0.029 2.00e-02 2.50e+03 pdb=" C8 G B 80 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G B 80 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 80 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B 80 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 80 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G B 80 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 80 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 80 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G B 80 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G B 80 " -0.002 2.00e-02 2.50e+03 ... (remaining 894 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 201 2.66 - 3.22: 7153 3.22 - 3.78: 15843 3.78 - 4.34: 20154 4.34 - 4.90: 28023 Nonbonded interactions: 71374 Sorted by model distance: nonbonded pdb=" ND1 HIS A 245 " pdb="MG MG A 502 " model vdw 2.103 2.250 nonbonded pdb=" OD1 ASP A 60 " pdb="MG MG A 501 " model vdw 2.105 2.170 nonbonded pdb=" NE2 HIS A 269 " pdb="MG MG A 502 " model vdw 2.125 2.250 nonbonded pdb=" NE2 HIS A 273 " pdb="MG MG A 502 " model vdw 2.213 2.250 nonbonded pdb=" SG CYS A 237 " pdb=" CE1 HIS A 268 " model vdw 2.442 2.896 ... (remaining 71369 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: 1.750 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.090 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 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 : 0.003 0.045 8659 Z= 0.230 Angle : 0.693 7.293 12607 Z= 0.564 Chirality : 0.055 0.307 1528 Planarity : 0.004 0.054 897 Dihedral : 21.609 178.670 4485 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 0.77 (0.40), residues: 493 helix: 1.78 (0.41), residues: 168 sheet: -0.47 (0.66), residues: 78 loop : 0.05 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 270 TYR 0.008 0.001 TYR A 5 PHE 0.014 0.001 PHE A 40 TRP 0.008 0.001 TRP A 278 HIS 0.002 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.23 ( 8655) covalent geometry : angle 0.69143 / 0.56 (12604) hydrogen bonds : bond 0.10414 / 5.90 ( 326) hydrogen bonds : angle 4.61506 / 3.17 ( 757) metal coordination : bond 0.02238 / 1.12 ( 4) metal coordination : angle 3.51701 / 1.85 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8757 (mp0) REVERT: A 76 GLU cc_start: 0.8726 (pm20) cc_final: 0.8321 (pm20) REVERT: A 196 PHE cc_start: 0.8832 (m-80) cc_final: 0.8397 (m-80) REVERT: A 213 ARG cc_start: 0.9017 (mtp85) cc_final: 0.8571 (mtp85) REVERT: A 224 GLU cc_start: 0.9152 (tp30) cc_final: 0.8837 (tm-30) REVERT: A 228 MET cc_start: 0.9252 (tpt) cc_final: 0.8932 (tmm) REVERT: A 231 ASP cc_start: 0.8927 (t0) cc_final: 0.8581 (t0) REVERT: A 243 HIS cc_start: 0.8330 (m-70) cc_final: 0.7783 (m90) REVERT: A 256 GLU cc_start: 0.9256 (mp0) cc_final: 0.8927 (mp0) REVERT: A 278 TRP cc_start: 0.8798 (m100) cc_final: 0.8496 (m100) REVERT: A 328 LEU cc_start: 0.9591 (mm) cc_final: 0.9376 (mt) REVERT: A 337 LYS cc_start: 0.9464 (mttm) cc_final: 0.9077 (mtmm) REVERT: A 356 LYS cc_start: 0.8756 (mttm) cc_final: 0.8476 (mtpm) REVERT: A 432 GLN cc_start: 0.8554 (mt0) cc_final: 0.8270 (mm-40) REVERT: A 465 GLN cc_start: 0.8459 (mt0) cc_final: 0.8168 (mm-40) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.7357 time to fit residues: 59.6568 Evaluate side-chains 56 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 130 GLN A 175 ASN A 207 GLN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.075019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.047096 restraints weight = 20074.468| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 2.10 r_work: 0.2437 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 8659 Z= 0.358 Angle : 0.639 6.449 12607 Z= 0.349 Chirality : 0.044 0.277 1528 Planarity : 0.005 0.076 897 Dihedral : 22.738 179.763 3456 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.63 % Allowed : 10.72 % Favored : 87.65 % 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: 0.62 (0.40), residues: 493 helix: 1.61 (0.41), residues: 169 sheet: -0.56 (0.65), residues: 78 loop : -0.01 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 461 TYR 0.016 0.002 TYR A 5 PHE 0.027 0.003 PHE A 236 TRP 0.010 0.002 TRP A 278 HIS 0.005 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.36 ( 8655) covalent geometry : angle 0.63564 / 0.35 (12604) hydrogen bonds : bond 0.05921 / 3.96 ( 326) hydrogen bonds : angle 4.02108 / 2.80 ( 757) metal coordination : bond 0.00787 / 0.39 ( 4) metal coordination : angle 3.99094 / 2.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.197 Fit side-chains REVERT: A 73 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8789 (mt-10) REVERT: A 213 ARG cc_start: 0.8999 (mtp85) cc_final: 0.8563 (mtp85) REVERT: A 219 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8236 (ttmm) REVERT: A 224 GLU cc_start: 0.9291 (tp30) cc_final: 0.8924 (tm-30) REVERT: A 228 MET cc_start: 0.9339 (tpt) cc_final: 0.8993 (tmm) REVERT: A 231 ASP cc_start: 0.9025 (t0) cc_final: 0.8602 (t0) REVERT: A 243 HIS cc_start: 0.8352 (m-70) cc_final: 0.7832 (m90) REVERT: A 256 GLU cc_start: 0.9217 (mp0) cc_final: 0.8969 (mp0) REVERT: A 277 GLU cc_start: 0.9337 (tm-30) cc_final: 0.9109 (tm-30) REVERT: A 278 TRP cc_start: 0.8895 (m100) cc_final: 0.8531 (m100) REVERT: A 281 ARG cc_start: 0.8337 (ttm110) cc_final: 0.7896 (ttm110) REVERT: A 328 LEU cc_start: 0.9630 (mm) cc_final: 0.9341 (mt) REVERT: A 331 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8928 (mt-10) REVERT: A 337 LYS cc_start: 0.9461 (mttm) cc_final: 0.8949 (mtmm) REVERT: A 356 LYS cc_start: 0.8799 (mttm) cc_final: 0.8531 (mtpm) REVERT: A 366 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8255 (mmm) REVERT: A 432 GLN cc_start: 0.8636 (mt0) cc_final: 0.8366 (mm-40) outliers start: 7 outliers final: 2 residues processed: 55 average time/residue: 0.7202 time to fit residues: 41.2927 Evaluate side-chains 53 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 366 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 37 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 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 = 0.3283 r_free = 0.3283 target = 0.076888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.049161 restraints weight = 19745.957| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 2.06 r_work: 0.2493 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2376 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8659 Z= 0.154 Angle : 0.508 6.709 12607 Z= 0.290 Chirality : 0.035 0.245 1528 Planarity : 0.004 0.054 897 Dihedral : 22.860 179.398 3456 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.17 % Allowed : 12.35 % Favored : 86.48 % 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: 0.69 (0.40), residues: 493 helix: 1.70 (0.41), residues: 171 sheet: -0.52 (0.64), residues: 78 loop : -0.01 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 33 TYR 0.012 0.001 TYR A 5 PHE 0.016 0.002 PHE A 40 TRP 0.004 0.001 TRP A 278 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 ( 8655) covalent geometry : angle 0.50522 / 0.29 (12604) hydrogen bonds : bond 0.04942 / 3.34 ( 326) hydrogen bonds : angle 3.74407 / 2.57 ( 757) metal coordination : bond 0.02300 / 1.15 ( 4) metal coordination : angle 3.66645 / 1.93 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8882 (mmm) cc_final: 0.8627 (mmm) REVERT: A 73 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8702 (mt-10) REVERT: A 76 GLU cc_start: 0.8802 (pm20) cc_final: 0.8529 (pm20) REVERT: A 84 GLU cc_start: 0.9347 (mt-10) cc_final: 0.9096 (mm-30) REVERT: A 146 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8403 (ptm160) REVERT: A 219 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8396 (ptmt) REVERT: A 224 GLU cc_start: 0.9292 (tp30) cc_final: 0.8934 (tm-30) REVERT: A 228 MET cc_start: 0.9326 (tpt) cc_final: 0.9048 (tpt) REVERT: A 231 ASP cc_start: 0.9027 (t0) cc_final: 0.8622 (t0) REVERT: A 256 GLU cc_start: 0.9256 (mp0) cc_final: 0.8993 (mp0) REVERT: A 277 GLU cc_start: 0.9449 (tm-30) cc_final: 0.9186 (tm-30) REVERT: A 278 TRP cc_start: 0.8894 (m100) cc_final: 0.8601 (m100) REVERT: A 281 ARG cc_start: 0.8518 (ttm110) cc_final: 0.8123 (ttm110) REVERT: A 328 LEU cc_start: 0.9627 (mm) cc_final: 0.9389 (mt) REVERT: A 337 LYS cc_start: 0.9468 (mttm) cc_final: 0.9089 (mtmm) REVERT: A 348 CYS cc_start: 0.9327 (m) cc_final: 0.9111 (m) REVERT: A 356 LYS cc_start: 0.8740 (mttm) cc_final: 0.8499 (mtpm) REVERT: A 432 GLN cc_start: 0.8679 (mt0) cc_final: 0.8383 (mm-40) REVERT: A 480 ARG cc_start: 0.9036 (tpp80) cc_final: 0.8633 (mpp80) outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 0.7238 time to fit residues: 42.9769 Evaluate side-chains 57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 302 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 30.0000 chunk 47 optimal weight: 0.0570 chunk 53 optimal weight: 10.0000 chunk 43 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.078691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.051127 restraints weight = 20058.942| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 2.14 r_work: 0.2542 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 8659 Z= 0.115 Angle : 0.479 8.053 12607 Z= 0.274 Chirality : 0.032 0.232 1528 Planarity : 0.004 0.053 897 Dihedral : 22.822 179.990 3456 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.70 % Allowed : 13.05 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.40), residues: 493 helix: 1.80 (0.41), residues: 171 sheet: -0.46 (0.61), residues: 88 loop : 0.01 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 213 TYR 0.008 0.001 TYR A 5 PHE 0.012 0.002 PHE A 40 TRP 0.004 0.001 TRP A 478 HIS 0.006 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 ( 8655) covalent geometry : angle 0.47411 / 0.27 (12604) hydrogen bonds : bond 0.04479 / 3.08 ( 326) hydrogen bonds : angle 3.52829 / 2.41 ( 757) metal coordination : bond 0.02558 / 1.28 ( 4) metal coordination : angle 4.66803 / 2.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.193 Fit side-chains REVERT: A 1 MET cc_start: 0.8803 (mmm) cc_final: 0.8522 (mmm) REVERT: A 73 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8608 (mt-10) REVERT: A 76 GLU cc_start: 0.8752 (pm20) cc_final: 0.8366 (pm20) REVERT: A 84 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8966 (mm-30) REVERT: A 195 ARG cc_start: 0.8682 (ptt90) cc_final: 0.8476 (ptt90) REVERT: A 213 ARG cc_start: 0.9023 (mtp-110) cc_final: 0.8686 (mtp85) REVERT: A 219 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8418 (ptmt) REVERT: A 224 GLU cc_start: 0.9288 (tp30) cc_final: 0.8935 (tm-30) REVERT: A 228 MET cc_start: 0.9311 (tpt) cc_final: 0.9016 (tpt) REVERT: A 231 ASP cc_start: 0.9010 (t0) cc_final: 0.8594 (t0) REVERT: A 256 GLU cc_start: 0.9195 (mp0) cc_final: 0.8902 (mp0) REVERT: A 266 GLU cc_start: 0.9087 (pm20) cc_final: 0.8738 (tm-30) REVERT: A 277 GLU cc_start: 0.9482 (tm-30) cc_final: 0.9165 (tm-30) REVERT: A 278 TRP cc_start: 0.8929 (m100) cc_final: 0.8626 (m100) REVERT: A 281 ARG cc_start: 0.8585 (ttm110) cc_final: 0.8156 (ttm110) REVERT: A 328 LEU cc_start: 0.9619 (mm) cc_final: 0.9294 (mt) REVERT: A 331 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8946 (mt-10) REVERT: A 337 LYS cc_start: 0.9437 (mttm) cc_final: 0.8920 (mtmm) REVERT: A 356 LYS cc_start: 0.8770 (mttm) cc_final: 0.8492 (mtpm) REVERT: A 407 ASP cc_start: 0.9192 (m-30) cc_final: 0.8937 (p0) REVERT: A 432 GLN cc_start: 0.8633 (mt0) cc_final: 0.8398 (mm110) REVERT: A 480 ARG cc_start: 0.8984 (tpp80) cc_final: 0.8345 (mpp80) outliers start: 3 outliers final: 4 residues processed: 58 average time/residue: 0.7461 time to fit residues: 45.1051 Evaluate side-chains 56 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 302 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 60 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.075686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.047798 restraints weight = 20307.615| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 2.12 r_work: 0.2451 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 8659 Z= 0.296 Angle : 0.585 6.866 12607 Z= 0.322 Chirality : 0.041 0.267 1528 Planarity : 0.004 0.057 897 Dihedral : 22.675 179.696 3456 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.63 % Allowed : 13.52 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.40), residues: 493 helix: 1.78 (0.41), residues: 169 sheet: -0.59 (0.64), residues: 78 loop : 0.03 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 324 TYR 0.020 0.002 TYR A 340 PHE 0.018 0.002 PHE A 40 TRP 0.006 0.001 TRP A 278 HIS 0.005 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.30 ( 8655) covalent geometry : angle 0.58255 / 0.32 (12604) hydrogen bonds : bond 0.05307 / 3.58 ( 326) hydrogen bonds : angle 3.63951 / 2.52 ( 757) metal coordination : bond 0.01076 / 0.54 ( 4) metal coordination : angle 3.27702 / 1.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8816 (mmm) cc_final: 0.8522 (mmm) REVERT: A 73 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8597 (mt-10) REVERT: A 76 GLU cc_start: 0.8765 (pm20) cc_final: 0.8473 (pm20) REVERT: A 84 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8950 (mm-30) REVERT: A 146 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8324 (ptm160) REVERT: A 213 ARG cc_start: 0.8992 (mtp-110) cc_final: 0.8651 (mtp85) REVERT: A 219 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8199 (ttmm) REVERT: A 224 GLU cc_start: 0.9259 (tp30) cc_final: 0.8934 (tm-30) REVERT: A 228 MET cc_start: 0.9299 (tpt) cc_final: 0.9005 (tpt) REVERT: A 231 ASP cc_start: 0.9047 (t0) cc_final: 0.8625 (t0) REVERT: A 256 GLU cc_start: 0.9201 (mp0) cc_final: 0.8957 (mp0) REVERT: A 259 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8704 (pt0) REVERT: A 277 GLU cc_start: 0.9495 (tm-30) cc_final: 0.9222 (tm-30) REVERT: A 278 TRP cc_start: 0.8860 (m100) cc_final: 0.8553 (m100) REVERT: A 281 ARG cc_start: 0.8576 (ttm110) cc_final: 0.8182 (ttm110) REVERT: A 328 LEU cc_start: 0.9630 (mm) cc_final: 0.9396 (mt) REVERT: A 337 LYS cc_start: 0.9449 (mttm) cc_final: 0.9063 (mtmm) REVERT: A 356 LYS cc_start: 0.8731 (mttm) cc_final: 0.8502 (mttm) REVERT: A 432 GLN cc_start: 0.8644 (mt0) cc_final: 0.8367 (mm-40) outliers start: 7 outliers final: 3 residues processed: 58 average time/residue: 0.7384 time to fit residues: 44.6607 Evaluate side-chains 56 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 302 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 30.0000 chunk 40 optimal weight: 0.0670 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 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 = 0.3315 r_free = 0.3315 target = 0.078489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.050887 restraints weight = 19957.723| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 2.13 r_work: 0.2529 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 8659 Z= 0.116 Angle : 0.478 6.963 12607 Z= 0.274 Chirality : 0.033 0.272 1528 Planarity : 0.004 0.053 897 Dihedral : 22.845 179.895 3456 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.40 % Allowed : 14.69 % Favored : 83.92 % 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: 0.69 (0.40), residues: 493 helix: 1.72 (0.41), residues: 171 sheet: -0.62 (0.60), residues: 88 loop : 0.06 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 324 TYR 0.008 0.001 TYR A 5 PHE 0.013 0.002 PHE A 40 TRP 0.004 0.001 TRP A 478 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.12 ( 8655) covalent geometry : angle 0.47378 / 0.27 (12604) hydrogen bonds : bond 0.04501 / 3.10 ( 326) hydrogen bonds : angle 3.43819 / 2.35 ( 757) metal coordination : bond 0.02908 / 1.45 ( 4) metal coordination : angle 3.94216 / 2.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8806 (mmm) cc_final: 0.8550 (mmm) REVERT: A 73 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8594 (mt-10) REVERT: A 76 GLU cc_start: 0.8779 (pm20) cc_final: 0.8545 (pm20) REVERT: A 84 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8957 (mm-30) REVERT: A 146 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8378 (ptm160) REVERT: A 213 ARG cc_start: 0.9012 (mtp-110) cc_final: 0.8658 (mtp85) REVERT: A 219 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8430 (ptmt) REVERT: A 224 GLU cc_start: 0.9263 (tp30) cc_final: 0.8912 (tm-30) REVERT: A 228 MET cc_start: 0.9291 (tpt) cc_final: 0.9029 (tpt) REVERT: A 231 ASP cc_start: 0.9067 (t0) cc_final: 0.8612 (t0) REVERT: A 256 GLU cc_start: 0.9231 (mp0) cc_final: 0.8905 (mp0) REVERT: A 266 GLU cc_start: 0.9138 (pm20) cc_final: 0.8709 (tm-30) REVERT: A 277 GLU cc_start: 0.9487 (tm-30) cc_final: 0.9235 (tm-30) REVERT: A 278 TRP cc_start: 0.8894 (m100) cc_final: 0.8630 (m100) REVERT: A 328 LEU cc_start: 0.9614 (mm) cc_final: 0.9372 (mt) REVERT: A 337 LYS cc_start: 0.9426 (mttm) cc_final: 0.9049 (mtmm) REVERT: A 356 LYS cc_start: 0.8767 (mttm) cc_final: 0.8536 (mtpm) REVERT: A 389 MET cc_start: 0.9396 (tpp) cc_final: 0.9158 (tpt) REVERT: A 407 ASP cc_start: 0.9190 (m-30) cc_final: 0.8985 (t0) REVERT: A 432 GLN cc_start: 0.8637 (mt0) cc_final: 0.8389 (mm-40) REVERT: A 480 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8575 (mpp80) outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 0.7931 time to fit residues: 45.3884 Evaluate side-chains 57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 480 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 chunk 41 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 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 = 0.3286 r_free = 0.3286 target = 0.077100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.049388 restraints weight = 20196.461| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.10 r_work: 0.2499 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8659 Z= 0.199 Angle : 0.512 7.293 12607 Z= 0.287 Chirality : 0.036 0.249 1528 Planarity : 0.004 0.056 897 Dihedral : 22.700 179.936 3456 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.33 % Allowed : 14.45 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.40), residues: 493 helix: 1.74 (0.41), residues: 171 sheet: -0.64 (0.60), residues: 88 loop : 0.10 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 324 TYR 0.012 0.001 TYR A 5 PHE 0.015 0.001 PHE A 40 TRP 0.005 0.001 TRP A 278 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.20 ( 8655) covalent geometry : angle 0.50962 / 0.29 (12604) hydrogen bonds : bond 0.04636 / 3.17 ( 326) hydrogen bonds : angle 3.46979 / 2.39 ( 757) metal coordination : bond 0.01512 / 0.76 ( 4) metal coordination : angle 3.09505 / 1.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8819 (mmm) cc_final: 0.8553 (mmm) REVERT: A 73 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8650 (mt-10) REVERT: A 76 GLU cc_start: 0.8779 (pm20) cc_final: 0.8451 (pm20) REVERT: A 84 GLU cc_start: 0.9292 (mt-10) cc_final: 0.9007 (mm-30) REVERT: A 146 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8342 (ptm160) REVERT: A 213 ARG cc_start: 0.9004 (mtp-110) cc_final: 0.8710 (mtp85) REVERT: A 219 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8408 (ptmt) REVERT: A 224 GLU cc_start: 0.9252 (tp30) cc_final: 0.8933 (tm-30) REVERT: A 228 MET cc_start: 0.9283 (tpt) cc_final: 0.9018 (tpt) REVERT: A 231 ASP cc_start: 0.9035 (t0) cc_final: 0.8627 (t0) REVERT: A 256 GLU cc_start: 0.9224 (mp0) cc_final: 0.8922 (mp0) REVERT: A 259 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8726 (pt0) REVERT: A 266 GLU cc_start: 0.9172 (pm20) cc_final: 0.8667 (tm-30) REVERT: A 277 GLU cc_start: 0.9475 (tm-30) cc_final: 0.9170 (tm-30) REVERT: A 278 TRP cc_start: 0.8877 (m100) cc_final: 0.8527 (m100) REVERT: A 281 ARG cc_start: 0.8511 (ttm110) cc_final: 0.8079 (ttm110) REVERT: A 328 LEU cc_start: 0.9620 (mm) cc_final: 0.9407 (mt) REVERT: A 337 LYS cc_start: 0.9443 (mttm) cc_final: 0.9053 (mtmm) REVERT: A 356 LYS cc_start: 0.8773 (mttm) cc_final: 0.8530 (mtpm) REVERT: A 407 ASP cc_start: 0.9220 (m-30) cc_final: 0.8956 (t0) REVERT: A 432 GLN cc_start: 0.8640 (mt0) cc_final: 0.8377 (mm-40) REVERT: A 480 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8545 (mpp80) outliers start: 10 outliers final: 5 residues processed: 56 average time/residue: 0.8022 time to fit residues: 46.7332 Evaluate side-chains 59 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 480 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 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 = 0.3299 r_free = 0.3299 target = 0.077696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.050034 restraints weight = 19928.202| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 2.12 r_work: 0.2513 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8659 Z= 0.144 Angle : 0.483 7.240 12607 Z= 0.276 Chirality : 0.034 0.244 1528 Planarity : 0.004 0.061 897 Dihedral : 22.743 179.976 3456 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.33 % Allowed : 15.38 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.40), residues: 493 helix: 1.76 (0.41), residues: 171 sheet: -0.66 (0.60), residues: 88 loop : 0.10 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 324 TYR 0.028 0.001 TYR A 340 PHE 0.015 0.001 PHE A 40 TRP 0.004 0.001 TRP A 278 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 8655) covalent geometry : angle 0.48060 / 0.28 (12604) hydrogen bonds : bond 0.04471 / 3.07 ( 326) hydrogen bonds : angle 3.43387 / 2.35 ( 757) metal coordination : bond 0.01635 / 0.82 ( 4) metal coordination : angle 3.11429 / 1.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.128 Fit side-chains REVERT: A 73 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8627 (mt-10) REVERT: A 76 GLU cc_start: 0.8801 (pm20) cc_final: 0.8389 (pm20) REVERT: A 84 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9016 (mm-30) REVERT: A 146 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8360 (ptm160) REVERT: A 192 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: A 213 ARG cc_start: 0.9025 (mtp-110) cc_final: 0.8724 (mtp85) REVERT: A 219 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8427 (ptmt) REVERT: A 224 GLU cc_start: 0.9265 (tp30) cc_final: 0.8931 (tm-30) REVERT: A 228 MET cc_start: 0.9301 (tpt) cc_final: 0.9034 (tpt) REVERT: A 231 ASP cc_start: 0.9026 (t0) cc_final: 0.8611 (t0) REVERT: A 256 GLU cc_start: 0.9228 (mp0) cc_final: 0.8925 (mp0) REVERT: A 259 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8744 (pt0) REVERT: A 266 GLU cc_start: 0.9150 (pm20) cc_final: 0.8676 (tm-30) REVERT: A 277 GLU cc_start: 0.9484 (tm-30) cc_final: 0.9166 (tm-30) REVERT: A 278 TRP cc_start: 0.8920 (m100) cc_final: 0.8565 (m100) REVERT: A 281 ARG cc_start: 0.8553 (ttm110) cc_final: 0.8075 (ttm110) REVERT: A 328 LEU cc_start: 0.9631 (mm) cc_final: 0.9328 (mt) REVERT: A 331 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8934 (mt-10) REVERT: A 337 LYS cc_start: 0.9427 (mttm) cc_final: 0.8915 (mtmm) REVERT: A 356 LYS cc_start: 0.8793 (mttm) cc_final: 0.8530 (mtpm) REVERT: A 407 ASP cc_start: 0.9207 (m-30) cc_final: 0.8967 (t0) REVERT: A 432 GLN cc_start: 0.8650 (mt0) cc_final: 0.8394 (mm-40) REVERT: A 480 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8541 (mpp80) outliers start: 10 outliers final: 5 residues processed: 57 average time/residue: 0.7462 time to fit residues: 44.2518 Evaluate side-chains 61 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 480 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 23 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 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 = 0.3302 r_free = 0.3302 target = 0.077955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.050314 restraints weight = 19992.027| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.12 r_work: 0.2513 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8659 Z= 0.143 Angle : 0.483 7.183 12607 Z= 0.274 Chirality : 0.034 0.241 1528 Planarity : 0.005 0.060 897 Dihedral : 22.731 179.806 3456 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.10 % Allowed : 15.62 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.40), residues: 493 helix: 1.76 (0.41), residues: 171 sheet: -0.65 (0.60), residues: 88 loop : 0.07 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 324 TYR 0.010 0.001 TYR A 5 PHE 0.014 0.001 PHE A 40 TRP 0.005 0.001 TRP A 278 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 ( 8655) covalent geometry : angle 0.48104 / 0.27 (12604) hydrogen bonds : bond 0.04401 / 3.03 ( 326) hydrogen bonds : angle 3.40299 / 2.33 ( 757) metal coordination : bond 0.01776 / 0.89 ( 4) metal coordination : angle 2.84911 / 1.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.162 Fit side-chains REVERT: A 73 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8607 (mt-10) REVERT: A 76 GLU cc_start: 0.8787 (pm20) cc_final: 0.8390 (pm20) REVERT: A 84 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8994 (mm-30) REVERT: A 146 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8280 (ptm160) REVERT: A 213 ARG cc_start: 0.9003 (mtp-110) cc_final: 0.8697 (mtp85) REVERT: A 219 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8410 (ptmt) REVERT: A 224 GLU cc_start: 0.9243 (tp30) cc_final: 0.8925 (tm-30) REVERT: A 228 MET cc_start: 0.9282 (tpt) cc_final: 0.9022 (tpt) REVERT: A 231 ASP cc_start: 0.9077 (t0) cc_final: 0.8657 (t0) REVERT: A 256 GLU cc_start: 0.9219 (mp0) cc_final: 0.8910 (mp0) REVERT: A 259 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8749 (pt0) REVERT: A 266 GLU cc_start: 0.9171 (pm20) cc_final: 0.8664 (tm-30) REVERT: A 277 GLU cc_start: 0.9482 (tm-30) cc_final: 0.9166 (tm-30) REVERT: A 278 TRP cc_start: 0.8879 (m100) cc_final: 0.8521 (m100) REVERT: A 281 ARG cc_start: 0.8536 (ttm110) cc_final: 0.8055 (ttm110) REVERT: A 328 LEU cc_start: 0.9616 (mm) cc_final: 0.9309 (mt) REVERT: A 331 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8927 (mt-10) REVERT: A 337 LYS cc_start: 0.9434 (mttm) cc_final: 0.8909 (mtmm) REVERT: A 356 LYS cc_start: 0.8770 (mttm) cc_final: 0.8505 (mtpm) REVERT: A 407 ASP cc_start: 0.9205 (m-30) cc_final: 0.8968 (t0) REVERT: A 432 GLN cc_start: 0.8608 (mt0) cc_final: 0.8353 (mm-40) REVERT: A 480 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8509 (mpp80) outliers start: 9 outliers final: 5 residues processed: 57 average time/residue: 0.7262 time to fit residues: 43.0410 Evaluate side-chains 60 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 480 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 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 = 0.3280 r_free = 0.3280 target = 0.076796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.048967 restraints weight = 20099.259| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 2.08 r_work: 0.2485 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2368 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8659 Z= 0.222 Angle : 0.535 7.559 12607 Z= 0.297 Chirality : 0.037 0.254 1528 Planarity : 0.005 0.059 897 Dihedral : 22.678 179.908 3456 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.33 % Allowed : 15.62 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.40), residues: 493 helix: 1.69 (0.41), residues: 171 sheet: -0.67 (0.60), residues: 88 loop : 0.13 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 251 TYR 0.020 0.001 TYR A 340 PHE 0.017 0.001 PHE A 40 TRP 0.007 0.001 TRP A 278 HIS 0.004 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.22 ( 8655) covalent geometry : angle 0.53329 / 0.30 (12604) hydrogen bonds : bond 0.04744 / 3.23 ( 326) hydrogen bonds : angle 3.48107 / 2.40 ( 757) metal coordination : bond 0.01407 / 0.70 ( 4) metal coordination : angle 2.82877 / 1.48 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.204 Fit side-chains REVERT: A 73 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8739 (mt-10) REVERT: A 76 GLU cc_start: 0.8887 (pm20) cc_final: 0.8495 (pm20) REVERT: A 84 GLU cc_start: 0.9429 (mt-10) cc_final: 0.9136 (mm-30) REVERT: A 146 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8434 (ptm160) REVERT: A 192 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: A 213 ARG cc_start: 0.9051 (mtp-110) cc_final: 0.8759 (mtp85) REVERT: A 219 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8414 (ptmt) REVERT: A 224 GLU cc_start: 0.9271 (tp30) cc_final: 0.8965 (tm-30) REVERT: A 228 MET cc_start: 0.9288 (tpt) cc_final: 0.9020 (tpt) REVERT: A 231 ASP cc_start: 0.9100 (t0) cc_final: 0.8721 (t0) REVERT: A 256 GLU cc_start: 0.9280 (mp0) cc_final: 0.8981 (mp0) REVERT: A 266 GLU cc_start: 0.9221 (pm20) cc_final: 0.8674 (tm-30) REVERT: A 277 GLU cc_start: 0.9477 (tm-30) cc_final: 0.9157 (tm-30) REVERT: A 278 TRP cc_start: 0.8851 (m100) cc_final: 0.8465 (m100) REVERT: A 281 ARG cc_start: 0.8534 (ttm110) cc_final: 0.8046 (ttm110) REVERT: A 328 LEU cc_start: 0.9633 (mm) cc_final: 0.9341 (mt) REVERT: A 331 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8984 (mt-10) REVERT: A 337 LYS cc_start: 0.9458 (mttm) cc_final: 0.8936 (mtmm) REVERT: A 356 LYS cc_start: 0.8795 (mttm) cc_final: 0.8525 (mtpm) REVERT: A 407 ASP cc_start: 0.9305 (m-30) cc_final: 0.9023 (t0) REVERT: A 432 GLN cc_start: 0.8711 (mt0) cc_final: 0.8417 (mm-40) REVERT: A 480 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8578 (mpp80) outliers start: 10 outliers final: 5 residues processed: 57 average time/residue: 0.7233 time to fit residues: 42.9190 Evaluate side-chains 60 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 480 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 57 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 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 = 0.3309 r_free = 0.3309 target = 0.078216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.050584 restraints weight = 20111.182| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 2.14 r_work: 0.2530 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8659 Z= 0.128 Angle : 0.482 7.642 12607 Z= 0.274 Chirality : 0.033 0.236 1528 Planarity : 0.004 0.060 897 Dihedral : 22.755 179.682 3456 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.10 % Allowed : 16.08 % Favored : 81.82 % 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: 0.68 (0.40), residues: 493 helix: 1.71 (0.41), residues: 171 sheet: -0.69 (0.60), residues: 88 loop : 0.08 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 251 TYR 0.009 0.001 TYR A 5 PHE 0.014 0.001 PHE A 40 TRP 0.004 0.001 TRP A 278 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 ( 8655) covalent geometry : angle 0.47994 / 0.27 (12604) hydrogen bonds : bond 0.04354 / 3.00 ( 326) hydrogen bonds : angle 3.39031 / 2.33 ( 757) metal coordination : bond 0.01874 / 0.94 ( 4) metal coordination : angle 2.70317 / 1.42 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2015.28 seconds wall clock time: 35 minutes 6.45 seconds (2106.45 seconds total)