Starting phenix.real_space_refine on Thu Jul 2 02:43:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h1j_34428/07_2026/8h1j_34428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h1j_34428/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8h1j_34428/07_2026/8h1j_34428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h1j_34428/07_2026/8h1j_34428.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8h1j_34428/07_2026/8h1j_34428.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h1j_34428/07_2026/8h1j_34428.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h1j_34428/07_2026/8h1j_34428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h1j_34428/07_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-dev-6108/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: {'RNA': 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: 1.53, per 1000 atoms: 0.27 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: 0.60 Conformation dependent library (CDL) restraints added in 259.2 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: 0.92 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: 1.17 Time building geometry restraints manager: 0.74 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 - 0.85: 8002 0.85 - 1.71: 751 1.71 - 2.56: 158 2.56 - 3.41: 32 3.41 - 4.27: 9 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 - 18.12: 2888 18.12 - 36.25: 301 36.25 - 54.37: 156 54.37 - 72.49: 34 72.49 - 90.62: 5 Dihedral angle restraints: 3384 sinusoidal: 2335 harmonic: 1049 Sorted by residual: dihedral pdb=" CA PHE A 35 " pdb=" C PHE A 35 " pdb=" N LEU A 36 " pdb=" CA LEU A 36 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.63e+00 dihedral pdb=" N LEU A 222 " pdb=" CA LEU A 222 " pdb=" CB LEU A 222 " pdb=" CG LEU A 222 " ideal model delta sinusoidal sigma weight residual -180.00 -120.80 -59.20 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS A 143 " pdb=" CB LYS A 143 " pdb=" CG LYS A 143 " pdb=" CD LYS A 143 " ideal model delta sinusoidal sigma weight residual -60.00 -118.40 58.40 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 3381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 768 0.033 - 0.067: 210 0.067 - 0.100: 70 0.100 - 0.134: 18 0.134 - 0.167: 4 Chirality restraints: 1070 Sorted by residual: chirality pdb=" C1' A B -88 " pdb=" O4' A B -88 " pdb=" C2' A B -88 " pdb=" N9 A B -88 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA PHE A 35 " pdb=" N PHE A 35 " pdb=" C PHE A 35 " pdb=" CB PHE A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" C3' C B-107 " pdb=" C4' C B-107 " pdb=" O3' C B-107 " pdb=" C2' C B-107 " both_signs ideal model delta sigma weight residual False -2.48 -2.62 0.14 2.00e-01 2.50e+01 5.13e-01 ... (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: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.670 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.130 ------------------------------------------------------------------------------- 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= 0.353 Angle : 0.915 54.546 8958 Z= 0.447 Chirality : 0.038 0.167 1070 Planarity : 0.004 0.044 648 Dihedral : 17.035 90.616 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 0.00517 / 0.35 ( 6167) covalent geometry : angle 0.57805 / 0.43 ( 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 : 0.147 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: 0.1276 time to fit residues: 10.5344 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 : 0.144 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.176455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134102 restraints weight = 8347.988| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.67 r_work: 0.3564 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6171 Z= 0.185 Angle : 0.652 19.396 8958 Z= 0.313 Chirality : 0.036 0.203 1070 Planarity : 0.004 0.045 648 Dihedral : 17.042 93.454 1998 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.87 % Allowed : 12.34 % 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: 2.18 (0.46), residues: 358 helix: 2.43 (0.37), residues: 175 sheet: 0.33 (0.61), residues: 81 loop : 0.80 (0.66), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 270 TYR 0.021 0.002 TYR A 118 PHE 0.022 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 0.00380 / 0.18 ( 6167) covalent geometry : angle 0.54727 / 0.31 ( 8952) hydrogen bonds : bond 0.06178 / 4.30 ( 310) hydrogen bonds : angle 4.03316 / 2.99 ( 727) metal coordination : bond 0.01012 / 0.50 ( 4) metal coordination : angle 13.68795 / 7.30 ( 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 49 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7565 (tp) cc_final: 0.7329 (tt) REVERT: A 48 LYS cc_start: 0.7451 (mmtt) cc_final: 0.6812 (pttt) REVERT: A 121 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: A 278 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6182 (pt0) REVERT: A 349 TRP cc_start: 0.7762 (p-90) cc_final: 0.6627 (p-90) outliers start: 15 outliers final: 12 residues processed: 48 average time/residue: 0.1046 time to fit residues: 6.3042 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 : 0.144 ------------------------------------------------------------------------------- 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 309 TYR 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: 9.9990 chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 40.0000 chunk 1 optimal weight: 0.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.173441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134938 restraints weight = 8231.407| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.57 r_work: 0.3449 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6171 Z= 0.257 Angle : 0.640 15.477 8958 Z= 0.325 Chirality : 0.039 0.223 1070 Planarity : 0.005 0.048 648 Dihedral : 17.323 93.961 1993 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.23 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: 1.74 (0.45), residues: 358 helix: 2.06 (0.37), residues: 175 sheet: -0.13 (0.63), residues: 75 loop : 0.80 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 221 TYR 0.023 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 0.00540 / 0.26 ( 6167) covalent geometry : angle 0.58527 / 0.32 ( 8952) hydrogen bonds : bond 0.06296 / 4.32 ( 310) hydrogen bonds : angle 3.92917 / 2.87 ( 727) metal coordination : bond 0.00913 / 0.46 ( 4) metal coordination : angle 10.05195 / 5.40 ( 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 40 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7648 (tp) cc_final: 0.7415 (tt) REVERT: A 48 LYS cc_start: 0.7656 (mmtt) cc_final: 0.6894 (pttt) REVERT: A 93 PHE cc_start: 0.8411 (t80) cc_final: 0.8036 (t80) REVERT: A 121 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8205 (mp10) REVERT: A 278 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5954 (pt0) REVERT: A 338 ASN cc_start: 0.6551 (p0) cc_final: 0.6072 (p0) REVERT: A 349 TRP cc_start: 0.7828 (p-90) cc_final: 0.6669 (p-90) outliers start: 14 outliers final: 10 residues processed: 40 average time/residue: 0.0638 time to fit residues: 3.5793 Evaluate side-chains 37 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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: 0.9980 chunk 11 optimal weight: 7.9990 chunk 45 optimal weight: 40.0000 chunk 36 optimal weight: 50.0000 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 48 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.177736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.139571 restraints weight = 8283.808| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.57 r_work: 0.3513 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6171 Z= 0.133 Angle : 0.515 11.540 8958 Z= 0.274 Chirality : 0.034 0.185 1070 Planarity : 0.004 0.045 648 Dihedral : 17.143 95.215 1993 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.90 % Allowed : 12.99 % 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: 2.20 (0.46), residues: 358 helix: 2.53 (0.38), residues: 175 sheet: 0.03 (0.66), residues: 70 loop : 0.83 (0.63), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.018 0.001 TYR A 309 PHE 0.017 0.002 PHE A 35 TRP 0.006 0.001 TRP A 70 HIS 0.001 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 6167) covalent geometry : angle 0.48615 / 0.27 ( 8952) hydrogen bonds : bond 0.04958 / 3.42 ( 310) hydrogen bonds : angle 3.58921 / 2.63 ( 727) metal coordination : bond 0.01018 / 0.51 ( 4) metal coordination : angle 6.55338 / 3.61 ( 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: 12 poor density : 27 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7525 (tp) cc_final: 0.7315 (tt) REVERT: A 48 LYS cc_start: 0.7652 (mmtt) cc_final: 0.6868 (pttt) REVERT: A 93 PHE cc_start: 0.8303 (t80) cc_final: 0.8033 (t80) REVERT: A 121 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: A 278 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6074 (pt0) REVERT: A 338 ASN cc_start: 0.6535 (p0) cc_final: 0.6106 (p0) REVERT: A 349 TRP cc_start: 0.7660 (p-90) cc_final: 0.6533 (p-90) outliers start: 12 outliers final: 10 residues processed: 39 average time/residue: 0.0805 time to fit residues: 4.2758 Evaluate side-chains 39 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.085 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 3 optimal weight: 8.9990 chunk 48 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 36 optimal weight: 50.0000 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.172582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.133871 restraints weight = 8416.221| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.63 r_work: 0.3438 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 6171 Z= 0.301 Angle : 0.633 11.233 8958 Z= 0.333 Chirality : 0.040 0.228 1070 Planarity : 0.005 0.048 648 Dihedral : 17.401 94.802 1993 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.14 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: 1.46 (0.45), residues: 358 helix: 1.93 (0.37), residues: 175 sheet: -0.36 (0.62), residues: 75 loop : 0.58 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 369 TYR 0.024 0.003 TYR A 118 PHE 0.027 0.003 PHE A 35 TRP 0.011 0.001 TRP A 141 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.30 ( 6167) covalent geometry : angle 0.61282 / 0.33 ( 8952) hydrogen bonds : bond 0.06242 / 4.25 ( 310) hydrogen bonds : angle 3.86157 / 2.80 ( 727) metal coordination : bond 0.00769 / 0.38 ( 4) metal coordination : angle 6.23322 / 3.37 ( 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 20 LEU cc_start: 0.7654 (tp) cc_final: 0.7432 (tt) REVERT: A 48 LYS cc_start: 0.7643 (mmtt) cc_final: 0.7004 (pttt) REVERT: A 121 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: A 278 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5962 (pt0) REVERT: A 338 ASN cc_start: 0.6689 (p0) cc_final: 0.6413 (p0) REVERT: A 349 TRP cc_start: 0.7769 (p-90) cc_final: 0.6686 (p-90) outliers start: 14 outliers final: 10 residues processed: 41 average time/residue: 0.0709 time to fit residues: 3.9130 Evaluate side-chains 39 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.175308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.137087 restraints weight = 8388.558| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.57 r_work: 0.3479 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6171 Z= 0.165 Angle : 0.523 9.686 8958 Z= 0.284 Chirality : 0.035 0.206 1070 Planarity : 0.004 0.047 648 Dihedral : 17.272 95.843 1993 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.87 % Allowed : 13.64 % 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: 1.65 (0.45), residues: 358 helix: 2.20 (0.38), residues: 175 sheet: -0.41 (0.64), residues: 72 loop : 0.54 (0.60), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 231 TYR 0.021 0.002 TYR A 309 PHE 0.020 0.002 PHE A 35 TRP 0.005 0.001 TRP A 141 HIS 0.002 0.001 HIS A 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 ( 6167) covalent geometry : angle 0.50657 / 0.28 ( 8952) hydrogen bonds : bond 0.05106 / 3.49 ( 310) hydrogen bonds : angle 3.65241 / 2.65 ( 727) metal coordination : bond 0.00557 / 0.28 ( 4) metal coordination : angle 5.03296 / 2.78 ( 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 46 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7595 (tp) cc_final: 0.7369 (tt) REVERT: A 48 LYS cc_start: 0.7642 (mmtt) cc_final: 0.6797 (pttt) REVERT: A 93 PHE cc_start: 0.8316 (t80) cc_final: 0.8109 (t80) REVERT: A 121 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: A 278 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6073 (pt0) REVERT: A 338 ASN cc_start: 0.6674 (p0) cc_final: 0.6451 (p0) REVERT: A 349 TRP cc_start: 0.7733 (p-90) cc_final: 0.6779 (p-90) outliers start: 15 outliers final: 11 residues processed: 46 average time/residue: 0.0750 time to fit residues: 4.5387 Evaluate side-chains 42 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 21 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 36 optimal weight: 50.0000 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.174328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136552 restraints weight = 8343.702| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.55 r_work: 0.3473 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2105 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= 0.184 Angle : 0.531 8.873 8958 Z= 0.287 Chirality : 0.036 0.202 1070 Planarity : 0.004 0.045 648 Dihedral : 17.216 95.659 1990 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.55 % Allowed : 13.96 % 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: 1.61 (0.45), residues: 358 helix: 2.18 (0.38), residues: 175 sheet: -0.36 (0.65), residues: 70 loop : 0.41 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 231 TYR 0.021 0.002 TYR A 309 PHE 0.023 0.002 PHE A 35 TRP 0.006 0.001 TRP A 141 HIS 0.004 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 6167) covalent geometry : angle 0.51779 / 0.29 ( 8952) hydrogen bonds : bond 0.05154 / 3.53 ( 310) hydrogen bonds : angle 3.62565 / 2.64 ( 727) metal coordination : bond 0.00499 / 0.25 ( 4) metal coordination : angle 4.52389 / 2.50 ( 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: 14 poor density : 29 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7614 (tp) cc_final: 0.7400 (tt) REVERT: A 48 LYS cc_start: 0.7654 (mmtt) cc_final: 0.6829 (pttt) REVERT: A 121 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: A 278 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6075 (pt0) REVERT: A 338 ASN cc_start: 0.6736 (p0) cc_final: 0.6202 (p0) REVERT: A 349 TRP cc_start: 0.7805 (p-90) cc_final: 0.6838 (p-90) outliers start: 14 outliers final: 11 residues processed: 43 average time/residue: 0.0805 time to fit residues: 4.6421 Evaluate side-chains 42 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 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: 20.0000 chunk 31 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 45 optimal weight: 40.0000 chunk 0 optimal weight: 9.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.171093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.132990 restraints weight = 8398.447| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.64 r_work: 0.3418 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 6171 Z= 0.318 Angle : 0.667 9.445 8958 Z= 0.352 Chirality : 0.042 0.252 1070 Planarity : 0.005 0.046 648 Dihedral : 17.586 95.655 1990 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.87 % Allowed : 13.64 % 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: 0.79 (0.44), residues: 358 helix: 1.53 (0.38), residues: 176 sheet: -0.90 (0.60), residues: 75 loop : 0.13 (0.59), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 108 TYR 0.023 0.003 TYR A 118 PHE 0.026 0.003 PHE A 35 TRP 0.011 0.002 TRP A 141 HIS 0.003 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.32 ( 6167) covalent geometry : angle 0.65493 / 0.35 ( 8952) hydrogen bonds : bond 0.06677 / 4.53 ( 310) hydrogen bonds : angle 3.95518 / 2.86 ( 727) metal coordination : bond 0.00694 / 0.35 ( 4) metal coordination : angle 4.94933 / 2.67 ( 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 44 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7674 (tp) cc_final: 0.7456 (tt) REVERT: A 48 LYS cc_start: 0.7638 (mmtt) cc_final: 0.6998 (pttt) REVERT: A 121 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8027 (mp10) REVERT: A 233 LYS cc_start: 0.7243 (pttt) cc_final: 0.6227 (mmtt) REVERT: A 278 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6184 (pt0) REVERT: A 338 ASN cc_start: 0.6878 (p0) cc_final: 0.6273 (p0) REVERT: A 349 TRP cc_start: 0.7818 (p-90) cc_final: 0.6671 (p-90) outliers start: 15 outliers final: 11 residues processed: 44 average time/residue: 0.0837 time to fit residues: 4.9054 Evaluate side-chains 42 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 33 optimal weight: 30.0000 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.174675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136618 restraints weight = 8382.182| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.56 r_work: 0.3471 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6171 Z= 0.167 Angle : 0.538 8.201 8958 Z= 0.291 Chirality : 0.036 0.215 1070 Planarity : 0.004 0.048 648 Dihedral : 17.378 96.861 1990 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 1.22 (0.45), residues: 358 helix: 1.97 (0.38), residues: 176 sheet: -0.86 (0.62), residues: 72 loop : 0.25 (0.59), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.021 0.002 TYR A 309 PHE 0.020 0.002 PHE A 35 TRP 0.006 0.001 TRP A 141 HIS 0.006 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 ( 6167) covalent geometry : angle 0.52813 / 0.29 ( 8952) hydrogen bonds : bond 0.05192 / 3.55 ( 310) hydrogen bonds : angle 3.66814 / 2.66 ( 727) metal coordination : bond 0.00446 / 0.23 ( 4) metal coordination : angle 4.06247 / 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: 15 poor density : 31 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7637 (tp) cc_final: 0.7418 (tt) REVERT: A 48 LYS cc_start: 0.7673 (mmtt) cc_final: 0.7009 (pttt) REVERT: A 121 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: A 233 LYS cc_start: 0.7103 (pttt) cc_final: 0.6054 (mmtt) REVERT: A 278 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.5945 (pt0) REVERT: A 338 ASN cc_start: 0.6853 (p0) cc_final: 0.6224 (p0) REVERT: A 349 TRP cc_start: 0.7829 (p-90) cc_final: 0.6673 (p-90) outliers start: 15 outliers final: 11 residues processed: 46 average time/residue: 0.0825 time to fit residues: 5.0236 Evaluate side-chains 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 42 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.173598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.135442 restraints weight = 8479.375| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.56 r_work: 0.3453 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2413 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= 0.227 Angle : 0.574 7.958 8958 Z= 0.307 Chirality : 0.038 0.220 1070 Planarity : 0.004 0.046 648 Dihedral : 17.438 96.322 1990 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.82 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: 1.05 (0.45), residues: 358 helix: 1.88 (0.38), residues: 176 sheet: -1.02 (0.61), residues: 72 loop : 0.13 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 231 TYR 0.022 0.002 TYR A 309 PHE 0.024 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 0.00482 / 0.23 ( 6167) covalent geometry : angle 0.56458 / 0.31 ( 8952) hydrogen bonds : bond 0.05505 / 3.75 ( 310) hydrogen bonds : angle 3.72853 / 2.71 ( 727) metal coordination : bond 0.00503 / 0.25 ( 4) metal coordination : angle 3.98399 / 2.19 ( 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 44 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7659 (tp) cc_final: 0.7440 (tt) REVERT: A 48 LYS cc_start: 0.7599 (mmtt) cc_final: 0.6863 (pttt) REVERT: A 121 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7913 (mp10) REVERT: A 233 LYS cc_start: 0.7082 (pttt) cc_final: 0.6039 (mmtt) REVERT: A 278 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.5949 (pt0) REVERT: A 338 ASN cc_start: 0.6718 (p0) cc_final: 0.5961 (p0) REVERT: A 349 TRP cc_start: 0.7772 (p-90) cc_final: 0.6638 (p-90) outliers start: 15 outliers final: 13 residues processed: 44 average time/residue: 0.0651 time to fit residues: 3.7171 Evaluate side-chains 44 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 47 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.172834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.135227 restraints weight = 8375.687| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.53 r_work: 0.3448 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6171 Z= 0.256 Angle : 0.598 7.731 8958 Z= 0.319 Chirality : 0.039 0.229 1070 Planarity : 0.005 0.046 648 Dihedral : 17.503 96.566 1990 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.02 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: 0.85 (0.44), residues: 358 helix: 1.73 (0.38), residues: 176 sheet: -1.01 (0.59), residues: 75 loop : -0.00 (0.59), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 231 TYR 0.022 0.002 TYR A 309 PHE 0.023 0.002 PHE A 35 TRP 0.009 0.001 TRP A 141 HIS 0.004 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.26 ( 6167) covalent geometry : angle 0.59013 / 0.32 ( 8952) hydrogen bonds : bond 0.05717 / 3.88 ( 310) hydrogen bonds : angle 3.79963 / 2.76 ( 727) metal coordination : bond 0.00565 / 0.29 ( 4) metal coordination : angle 3.86731 / 2.12 ( 6) =============================================================================== Job complete usr+sys time: 1230.36 seconds wall clock time: 21 minutes 53.61 seconds (1313.61 seconds total)