Starting phenix.real_space_refine on Tue Aug 4 18:34:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h1j_34428/08_2026/8h1j_34428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h1j_34428/08_2026/8h1j_34428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8h1j_34428/08_2026/8h1j_34428.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h1j_34428/08_2026/8h1j_34428.cif" model { file = "/net/cci-nas-00/data/ceres_data/8h1j_34428/08_2026/8h1j_34428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h1j_34428/08_2026/8h1j_34428.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h1j_34428/08_2026/8h1j_34428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h1j_34428/08_2026/8h1j_34428.map" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.134 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 134 5.49 5 S 6 5.16 5 C 3147 2.51 5 N 1063 2.21 5 O 1422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 5773 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2930 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain breaks: 1 Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 454 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "B" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2185 Classifications: {'RNAv2': 102} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 52, 'rna3p_pyr': 43} Link IDs: {'rna2p': 7, 'rna3p': 94} Chain breaks: 2 Chain: "D" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} 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 2567 SG CYS A 331 56.562 13.710 50.711 1.00192.35 S ATOM 2591 SG CYS A 334 56.015 10.341 49.439 1.00215.36 S ATOM 2728 SG CYS A 351 54.453 10.050 52.311 1.00222.37 S ATOM 2749 SG CYS A 354 57.190 11.215 52.766 1.00225.00 S Time building chain proxies: 1.07, per 1000 atoms: 0.19 Number of scatterers: 5773 At special positions: 0 Unit cell: (77.024, 102.256, 104.912, 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 6 16.00 P 134 15.00 O 1422 8.00 N 1063 7.00 C 3147 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: 0.32 Conformation dependent library (CDL) restraints added in 198.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 331 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 351 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 354 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 334 " Number of angles added : 6 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 674 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 4 sheets defined 48.6% alpha, 20.4% beta 57 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 14 through 47 Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.857A pdb=" N LEU A 71 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 removed outlier: 3.711A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 232 Processing helix chain 'A' and resid 236 through 271 Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 360 through 377 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.935A pdb=" N GLU A 116 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N LYS A 153 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N GLU A 176 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU A 155 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N GLU A 174 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL A 157 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU A 172 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL A 159 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER A 170 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ARG A 161 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU A 168 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 163 " --> pdb=" O HIS A 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR A 167 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 10 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS A 143 " --> pdb=" O TYR A 12 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 128 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.761A pdb=" N PHE A 186 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLU A 278 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU A 273 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N SER A 319 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE A 275 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL A 321 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR A 277 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 201 Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 351 removed outlier: 3.918A pdb=" N TRP A 349 " --> pdb=" O HIS A 358 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1031 1.33 - 1.45: 2200 1.45 - 1.57: 2666 1.57 - 1.69: 263 1.69 - 1.81: 7 Bond restraints: 6167 Sorted by residual: bond pdb=" C3' DA C 9 " pdb=" C2' DA C 9 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.44e+00 bond pdb=" C5 DC D -8 " pdb=" C6 DC D -8 " ideal model delta sigma weight residual 1.339 1.360 -0.021 8.00e-03 1.56e+04 7.19e+00 bond pdb=" C5 DC C 16 " pdb=" C6 DC C 16 " ideal model delta sigma weight residual 1.339 1.360 -0.021 8.00e-03 1.56e+04 6.98e+00 bond pdb=" C5 DC C 14 " pdb=" C6 DC C 14 " ideal model delta sigma weight residual 1.339 1.360 -0.021 8.00e-03 1.56e+04 6.93e+00 bond pdb=" C3' DG C 10 " pdb=" C2' DG C 10 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.46e+00 ... (remaining 6162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 8116 1.13 - 2.26: 533 2.26 - 3.39: 260 3.39 - 4.52: 33 4.52 - 5.65: 10 Bond angle restraints: 8952 Sorted by residual: angle pdb=" N3 DT D -7 " pdb=" C4 DT D -7 " pdb=" O4 DT D -7 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT D -9 " pdb=" C4 DT D -9 " pdb=" O4 DT D -9 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT D -4 " pdb=" C4 DT D -4 " pdb=" O4 DT D -4 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT D -10 " pdb=" C4 DT D -10 " pdb=" O4 DT D -10 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 angle pdb=" N3 DT C 18 " pdb=" C4 DT C 18 " pdb=" O4 DT C 18 " ideal model delta sigma weight residual 119.90 122.29 -2.39 6.00e-01 2.78e+00 1.59e+01 ... (remaining 8947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 2728 17.37 - 34.75: 339 34.75 - 52.12: 223 52.12 - 69.49: 84 69.49 - 86.86: 10 Dihedral angle restraints: 3384 sinusoidal: 2335 harmonic: 1049 Sorted by residual: dihedral pdb=" C4' A B -76 " pdb=" C3' A B -76 " pdb=" C2' A B -76 " pdb=" C1' A B -76 " ideal model delta sinusoidal sigma weight residual 36.34 -39.12 75.47 1 3.10e+00 1.04e-01 7.48e+02 dihedral pdb=" C4' G B 1 " pdb=" C3' G B 1 " pdb=" C2' G B 1 " pdb=" C1' G B 1 " ideal model delta sinusoidal sigma weight residual 36.35 -35.82 72.17 1 3.10e+00 1.04e-01 6.93e+02 dihedral pdb=" C4' C B -39 " pdb=" C3' C B -39 " pdb=" C2' C B -39 " pdb=" C1' C B -39 " ideal model delta sinusoidal sigma weight residual 36.34 -35.80 72.15 1 3.10e+00 1.04e-01 6.93e+02 ... (remaining 3381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 842 0.060 - 0.120: 104 0.120 - 0.180: 10 0.180 - 0.239: 92 0.239 - 0.299: 22 Chirality restraints: 1070 Sorted by residual: chirality pdb=" C3' A B -76 " pdb=" C4' A B -76 " pdb=" O3' A B -76 " pdb=" C2' A B -76 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C2' G B 1 " pdb=" C3' G B 1 " pdb=" O2' G B 1 " pdb=" C1' G B 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C3' G B 1 " pdb=" C4' G B 1 " pdb=" O3' G B 1 " pdb=" C2' G B 1 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1067 not shown) Planarity restraints: 648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA C 21 " -0.029 2.00e-02 2.50e+03 1.26e-02 4.34e+00 pdb=" N9 DA C 21 " 0.005 2.00e-02 2.50e+03 pdb=" C8 DA C 21 " 0.010 2.00e-02 2.50e+03 pdb=" N7 DA C 21 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DA C 21 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DA C 21 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA C 21 " -0.022 2.00e-02 2.50e+03 pdb=" N1 DA C 21 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA C 21 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA C 21 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA C 21 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B -96 " -0.026 2.00e-02 2.50e+03 1.09e-02 3.58e+00 pdb=" N9 G B -96 " 0.025 2.00e-02 2.50e+03 pdb=" C8 G B -96 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B -96 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B -96 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B -96 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G B -96 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G B -96 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G B -96 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B -96 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G B -96 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G B -96 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 106 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A 107 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " 0.025 5.00e-02 4.00e+02 ... (remaining 645 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1045 2.77 - 3.30: 5147 3.30 - 3.83: 11172 3.83 - 4.37: 13054 4.37 - 4.90: 18820 Nonbonded interactions: 49238 Sorted by model distance: nonbonded pdb=" N2 G B-112 " pdb=" N6 A B -86 " model vdw 2.232 2.560 nonbonded pdb=" O2' G B-111 " pdb=" N4 C B -85 " model vdw 2.293 3.120 nonbonded pdb=" NH1 ARG A 270 " pdb=" OP1 A B -1 " model vdw 2.303 3.120 nonbonded pdb=" NH1 ARG A 110 " pdb=" OP1 C B 5 " model vdw 2.347 3.120 nonbonded pdb=" OG1 THR A 114 " pdb=" OP1 DA C 8 " model vdw 2.356 3.040 ... (remaining 49233 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: 0.040 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.040 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: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 6171 Z= 0.357 Angle : 1.043 54.546 8958 Z= 0.472 Chirality : 0.084 0.299 1070 Planarity : 0.004 0.044 648 Dihedral : 19.758 86.862 2710 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 5.19 % Allowed : 9.74 % Favored : 85.06 % 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: 2.19 (0.45), residues: 358 helix: 2.39 (0.37), residues: 173 sheet: 0.49 (0.60), residues: 81 loop : 0.79 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.024 0.002 TYR A 309 PHE 0.026 0.002 PHE A 35 TRP 0.007 0.001 TRP A 349 HIS 0.005 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.35 ( 6167) covalent geometry : angle 0.76496 / 0.45 ( 8952) hydrogen bonds : bond 0.14264 / 9.65 ( 310) hydrogen bonds : angle 5.30813 / 3.87 ( 727) metal coordination : bond 0.04283 / 2.25 ( 4) metal coordination : angle 27.42998 / 14.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.6814 (tp) cc_final: 0.6588 (tt) REVERT: A 48 LYS cc_start: 0.7205 (mmtt) cc_final: 0.6282 (pttt) REVERT: A 58 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7176 (tt0) REVERT: A 95 ARG cc_start: 0.5955 (ttt90) cc_final: 0.5609 (ttp-110) REVERT: A 121 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: A 149 ASP cc_start: 0.7883 (m-30) cc_final: 0.7430 (t70) REVERT: A 175 VAL cc_start: 0.7996 (t) cc_final: 0.7731 (m) REVERT: A 205 ARG cc_start: 0.6711 (mtt180) cc_final: 0.6226 (mtm110) REVERT: A 207 LYS cc_start: 0.7279 (tptm) cc_final: 0.6720 (ttmt) REVERT: A 210 GLN cc_start: 0.8743 (pt0) cc_final: 0.8465 (pt0) REVERT: A 233 LYS cc_start: 0.5881 (OUTLIER) cc_final: 0.5044 (mmtt) REVERT: A 245 LYS cc_start: 0.7923 (tttt) cc_final: 0.7696 (mttm) REVERT: A 248 ARG cc_start: 0.7397 (mmm-85) cc_final: 0.7114 (tpt-90) REVERT: A 252 ARG cc_start: 0.6381 (mtt180) cc_final: 0.5898 (mtp-110) REVERT: A 349 TRP cc_start: 0.7735 (p-90) cc_final: 0.5851 (p-90) REVERT: A 367 ASN cc_start: 0.6759 (m-40) cc_final: 0.6497 (m-40) REVERT: A 371 GLU cc_start: 0.7470 (tp30) cc_final: 0.7177 (tp30) outliers start: 16 outliers final: 7 residues processed: 69 average time/residue: 0.0929 time to fit residues: 7.7245 Evaluate side-chains 44 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 341 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN A 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.176601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.134561 restraints weight = 8399.047| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.67 r_work: 0.3571 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6171 Z= 0.226 Angle : 1.075 19.890 8958 Z= 0.445 Chirality : 0.091 1.251 1070 Planarity : 0.005 0.045 648 Dihedral : 19.533 137.959 1998 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.55 % Allowed : 12.34 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.46), residues: 358 helix: 2.43 (0.37), residues: 175 sheet: 0.32 (0.62), residues: 81 loop : 0.80 (0.66), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 119 TYR 0.021 0.002 TYR A 118 PHE 0.023 0.002 PHE A 35 TRP 0.006 0.001 TRP A 70 HIS 0.005 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.23 ( 6167) covalent geometry : angle 1.01516 / 0.44 ( 8952) hydrogen bonds : bond 0.06296 / 4.43 ( 310) hydrogen bonds : angle 4.01998 / 2.98 ( 727) metal coordination : bond 0.01356 / 0.68 ( 4) metal coordination : angle 13.72532 / 7.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7617 (tp) cc_final: 0.7361 (tt) REVERT: A 48 LYS cc_start: 0.7448 (mmtt) cc_final: 0.6726 (pttt) REVERT: A 121 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8154 (mp10) REVERT: A 205 ARG cc_start: 0.7258 (mtt180) cc_final: 0.6897 (mtm110) REVERT: A 210 GLN cc_start: 0.8857 (pt0) cc_final: 0.8634 (pt0) REVERT: A 248 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7737 (tpt-90) REVERT: A 278 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6187 (pt0) REVERT: A 349 TRP cc_start: 0.7696 (p-90) cc_final: 0.6406 (p-90) outliers start: 14 outliers final: 11 residues processed: 47 average time/residue: 0.0706 time to fit residues: 4.1987 Evaluate side-chains 40 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 37 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 30.0000 chunk 1 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.174417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132028 restraints weight = 8349.502| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.67 r_work: 0.3537 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6171 Z= 0.260 Angle : 0.925 14.619 8958 Z= 0.399 Chirality : 0.075 1.178 1070 Planarity : 0.005 0.047 648 Dihedral : 19.420 147.180 1993 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.87 % Allowed : 12.99 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.45), residues: 358 helix: 2.14 (0.37), residues: 175 sheet: -0.10 (0.64), residues: 75 loop : 0.78 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.024 0.002 TYR A 118 PHE 0.026 0.002 PHE A 35 TRP 0.007 0.001 TRP A 141 HIS 0.005 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.26 ( 6167) covalent geometry : angle 0.89579 / 0.40 ( 8952) hydrogen bonds : bond 0.06796 / 4.62 ( 310) hydrogen bonds : angle 3.88634 / 2.85 ( 727) metal coordination : bond 0.02628 / 1.30 ( 4) metal coordination : angle 8.91929 / 4.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7623 (tp) cc_final: 0.7412 (tt) REVERT: A 48 LYS cc_start: 0.7729 (mmtt) cc_final: 0.6956 (pttt) REVERT: A 93 PHE cc_start: 0.8301 (t80) cc_final: 0.7980 (t80) REVERT: A 121 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8040 (mp10) REVERT: A 278 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.6047 (pt0) REVERT: A 338 ASN cc_start: 0.6472 (p0) cc_final: 0.6205 (p0) REVERT: A 349 TRP cc_start: 0.7897 (p-90) cc_final: 0.6774 (p-90) outliers start: 15 outliers final: 10 residues processed: 41 average time/residue: 0.0583 time to fit residues: 3.2231 Evaluate side-chains 38 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 45 optimal weight: 30.0000 chunk 36 optimal weight: 50.0000 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 30.0000 chunk 25 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.176297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139401 restraints weight = 8496.283| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.56 r_work: 0.3470 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6171 Z= 0.198 Angle : 0.841 12.335 8958 Z= 0.366 Chirality : 0.065 0.771 1070 Planarity : 0.004 0.045 648 Dihedral : 19.244 146.674 1993 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.55 % Allowed : 12.66 % Favored : 82.79 % 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: 1.95 (0.45), residues: 358 helix: 2.31 (0.38), residues: 175 sheet: 0.03 (0.64), residues: 73 loop : 0.67 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.021 0.002 TYR A 309 PHE 0.023 0.002 PHE A 35 TRP 0.006 0.001 TRP A 70 HIS 0.004 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 ( 6167) covalent geometry : angle 0.82590 / 0.36 ( 8952) hydrogen bonds : bond 0.05867 / 4.05 ( 310) hydrogen bonds : angle 3.70378 / 2.71 ( 727) metal coordination : bond 0.01358 / 0.68 ( 4) metal coordination : angle 6.26426 / 3.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7689 (mmtt) cc_final: 0.7037 (pttt) REVERT: A 121 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7836 (mp10) REVERT: A 278 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6367 (pt0) REVERT: A 338 ASN cc_start: 0.6529 (p0) cc_final: 0.6102 (p0) REVERT: A 349 TRP cc_start: 0.7823 (p-90) cc_final: 0.6947 (p-90) outliers start: 14 outliers final: 11 residues processed: 39 average time/residue: 0.0663 time to fit residues: 3.4648 Evaluate side-chains 37 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 48 optimal weight: 30.0000 chunk 26 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 36 optimal weight: 50.0000 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.173112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.135932 restraints weight = 8578.280| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.56 r_work: 0.3422 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6171 Z= 0.288 Angle : 0.902 11.579 8958 Z= 0.394 Chirality : 0.069 0.807 1070 Planarity : 0.005 0.047 648 Dihedral : 19.359 146.789 1993 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.55 % Allowed : 13.31 % Favored : 82.14 % 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: 1.34 (0.44), residues: 358 helix: 1.87 (0.38), residues: 175 sheet: -0.45 (0.62), residues: 75 loop : 0.47 (0.59), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 39 TYR 0.023 0.002 TYR A 309 PHE 0.025 0.003 PHE A 35 TRP 0.009 0.001 TRP A 141 HIS 0.005 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.29 ( 6167) covalent geometry : angle 0.88943 / 0.39 ( 8952) hydrogen bonds : bond 0.06569 / 4.49 ( 310) hydrogen bonds : angle 3.85930 / 2.80 ( 727) metal coordination : bond 0.00730 / 0.37 ( 4) metal coordination : angle 5.96017 / 3.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 27 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7151 (pttt) REVERT: A 121 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: A 278 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6224 (pt0) REVERT: A 338 ASN cc_start: 0.6672 (p0) cc_final: 0.6216 (p0) REVERT: A 349 TRP cc_start: 0.7945 (p-90) cc_final: 0.6986 (p-90) outliers start: 14 outliers final: 10 residues processed: 41 average time/residue: 0.0690 time to fit residues: 3.8371 Evaluate side-chains 38 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.176824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.140085 restraints weight = 8559.225| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.56 r_work: 0.3476 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6171 Z= 0.168 Angle : 0.793 10.023 8958 Z= 0.347 Chirality : 0.063 0.638 1070 Planarity : 0.004 0.047 648 Dihedral : 19.233 146.025 1993 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.55 % Allowed : 13.31 % Favored : 82.14 % 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: 1.64 (0.45), residues: 358 helix: 2.19 (0.38), residues: 175 sheet: -0.38 (0.64), residues: 72 loop : 0.48 (0.59), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 252 TYR 0.021 0.002 TYR A 309 PHE 0.019 0.002 PHE A 35 TRP 0.005 0.001 TRP A 141 HIS 0.004 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 ( 6167) covalent geometry : angle 0.78361 / 0.35 ( 8952) hydrogen bonds : bond 0.05530 / 3.83 ( 310) hydrogen bonds : angle 3.62898 / 2.65 ( 727) metal coordination : bond 0.00503 / 0.25 ( 4) metal coordination : angle 4.66132 / 2.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 28 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7002 (pttt) REVERT: A 93 PHE cc_start: 0.8157 (t80) cc_final: 0.7931 (t80) REVERT: A 121 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7680 (mp10) REVERT: A 278 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6344 (pt0) REVERT: A 338 ASN cc_start: 0.6668 (p0) cc_final: 0.6467 (p0) REVERT: A 349 TRP cc_start: 0.7895 (p-90) cc_final: 0.7007 (p-90) outliers start: 14 outliers final: 11 residues processed: 42 average time/residue: 0.0861 time to fit residues: 4.5977 Evaluate side-chains 39 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 26 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 21 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 36 optimal weight: 50.0000 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.173695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.136894 restraints weight = 8596.324| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.56 r_work: 0.3447 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6171 Z= 0.263 Angle : 0.871 10.553 8958 Z= 0.382 Chirality : 0.067 0.758 1070 Planarity : 0.005 0.046 648 Dihedral : 19.279 145.235 1990 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.19 % Allowed : 12.34 % Favored : 82.47 % 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: 1.23 (0.45), residues: 358 helix: 1.81 (0.38), residues: 176 sheet: -0.53 (0.61), residues: 75 loop : 0.37 (0.60), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 39 TYR 0.022 0.002 TYR A 309 PHE 0.026 0.003 PHE A 35 TRP 0.009 0.001 TRP A 141 HIS 0.004 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.26 ( 6167) covalent geometry : angle 0.86303 / 0.38 ( 8952) hydrogen bonds : bond 0.06251 / 4.27 ( 310) hydrogen bonds : angle 3.79148 / 2.76 ( 727) metal coordination : bond 0.00596 / 0.30 ( 4) metal coordination : angle 4.70491 / 2.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 27 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7156 (pttt) REVERT: A 121 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7755 (mp10) REVERT: A 278 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6336 (pt0) REVERT: A 349 TRP cc_start: 0.7914 (p-90) cc_final: 0.6959 (p-90) outliers start: 16 outliers final: 13 residues processed: 43 average time/residue: 0.0614 time to fit residues: 3.5171 Evaluate side-chains 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 45 optimal weight: 40.0000 chunk 0 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.174018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137158 restraints weight = 8498.901| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.56 r_work: 0.3394 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6171 Z= 0.242 Angle : 0.845 10.254 8958 Z= 0.371 Chirality : 0.066 0.712 1070 Planarity : 0.004 0.047 648 Dihedral : 19.282 144.726 1990 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.87 % Allowed : 13.31 % 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: 1.12 (0.45), residues: 358 helix: 1.81 (0.38), residues: 176 sheet: -0.85 (0.62), residues: 72 loop : 0.31 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 29 TYR 0.022 0.002 TYR A 309 PHE 0.023 0.002 PHE A 35 TRP 0.008 0.001 TRP A 141 HIS 0.005 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.24 ( 6167) covalent geometry : angle 0.83803 / 0.37 ( 8952) hydrogen bonds : bond 0.05976 / 4.10 ( 310) hydrogen bonds : angle 3.75176 / 2.73 ( 727) metal coordination : bond 0.00509 / 0.26 ( 4) metal coordination : angle 4.21054 / 2.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7138 (pttt) REVERT: A 121 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7717 (mp10) REVERT: A 233 LYS cc_start: 0.7495 (pttt) cc_final: 0.6584 (mmtt) REVERT: A 278 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.6084 (pt0) REVERT: A 349 TRP cc_start: 0.7936 (p-90) cc_final: 0.6790 (p-90) outliers start: 15 outliers final: 12 residues processed: 43 average time/residue: 0.0618 time to fit residues: 3.5422 Evaluate side-chains 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.173664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136782 restraints weight = 8536.577| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.56 r_work: 0.3452 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6171 Z= 0.251 Angle : 0.856 10.286 8958 Z= 0.377 Chirality : 0.066 0.724 1070 Planarity : 0.005 0.047 648 Dihedral : 19.303 144.701 1990 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 5.52 % Allowed : 12.99 % Favored : 81.49 % 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: 1.03 (0.44), residues: 358 helix: 1.78 (0.38), residues: 176 sheet: -0.94 (0.62), residues: 72 loop : 0.24 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 39 TYR 0.022 0.002 TYR A 309 PHE 0.023 0.002 PHE A 35 TRP 0.008 0.001 TRP A 141 HIS 0.004 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.25 ( 6167) covalent geometry : angle 0.84963 / 0.38 ( 8952) hydrogen bonds : bond 0.06020 / 4.12 ( 310) hydrogen bonds : angle 3.77417 / 2.75 ( 727) metal coordination : bond 0.00552 / 0.28 ( 4) metal coordination : angle 4.11093 / 2.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7185 (pttt) REVERT: A 121 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: A 233 LYS cc_start: 0.7572 (pttt) cc_final: 0.6699 (mmtt) REVERT: A 278 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.6154 (pt0) REVERT: A 338 ASN cc_start: 0.6918 (p0) cc_final: 0.6573 (p0) REVERT: A 349 TRP cc_start: 0.7997 (p-90) cc_final: 0.6980 (p-90) outliers start: 17 outliers final: 13 residues processed: 46 average time/residue: 0.0818 time to fit residues: 4.9035 Evaluate side-chains 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.172439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.135781 restraints weight = 8649.255| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.56 r_work: 0.3433 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6171 Z= 0.298 Angle : 0.907 10.603 8958 Z= 0.400 Chirality : 0.069 0.775 1070 Planarity : 0.005 0.047 648 Dihedral : 19.391 144.215 1990 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.19 % Allowed : 12.66 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.44), residues: 358 helix: 1.53 (0.38), residues: 176 sheet: -1.02 (0.60), residues: 75 loop : -0.01 (0.58), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 38 TYR 0.023 0.002 TYR A 309 PHE 0.024 0.003 PHE A 35 TRP 0.010 0.001 TRP A 141 HIS 0.004 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.30 ( 6167) covalent geometry : angle 0.90017 / 0.40 ( 8952) hydrogen bonds : bond 0.06493 / 4.41 ( 310) hydrogen bonds : angle 3.91192 / 2.85 ( 727) metal coordination : bond 0.00609 / 0.31 ( 4) metal coordination : angle 4.25101 / 2.31 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 29 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7633 (mmtt) cc_final: 0.7195 (pttt) REVERT: A 121 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7762 (mp10) REVERT: A 233 LYS cc_start: 0.7578 (pttt) cc_final: 0.6711 (mmtt) REVERT: A 278 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6216 (pt0) REVERT: A 349 TRP cc_start: 0.8061 (p-90) cc_final: 0.6968 (p-90) outliers start: 16 outliers final: 14 residues processed: 45 average time/residue: 0.0874 time to fit residues: 5.2057 Evaluate side-chains 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 27 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 48 optimal weight: 30.0000 chunk 43 optimal weight: 10.0000 chunk 31 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 overall best weight: 6.7388 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.172718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.135737 restraints weight = 8533.490| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.61 r_work: 0.3426 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 6171 Z= 0.284 Angle : 0.893 10.517 8958 Z= 0.394 Chirality : 0.069 0.755 1070 Planarity : 0.005 0.048 648 Dihedral : 19.387 144.248 1990 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.87 % Allowed : 13.31 % 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: 0.65 (0.44), residues: 358 helix: 1.56 (0.38), residues: 176 sheet: -1.28 (0.61), residues: 72 loop : -0.00 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 38 TYR 0.023 0.002 TYR A 309 PHE 0.024 0.003 PHE A 35 TRP 0.009 0.001 TRP A 141 HIS 0.005 0.002 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.28 ( 6167) covalent geometry : angle 0.88685 / 0.39 ( 8952) hydrogen bonds : bond 0.06335 / 4.31 ( 310) hydrogen bonds : angle 3.90271 / 2.84 ( 727) metal coordination : bond 0.00547 / 0.28 ( 4) metal coordination : angle 4.00241 / 2.19 ( 6) =============================================================================== Job complete usr+sys time: 1092.82 seconds wall clock time: 19 minutes 24.97 seconds (1164.97 seconds total)