Starting phenix.real_space_refine on Tue Mar 3 14:22:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h1j_34428/03_2026/8h1j_34428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h1j_34428/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h1j_34428/03_2026/8h1j_34428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h1j_34428/03_2026/8h1j_34428.map" model { file = "/net/cci-nas-00/data/ceres_data/8h1j_34428/03_2026/8h1j_34428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h1j_34428/03_2026/8h1j_34428.cif" } 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-5986/lib/python3.9/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: 1.57, 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: 0.81 Conformation dependent library (CDL) restraints added in 104.2 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: 0.83 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: 1.25 Time building geometry restraints manager: 0.93 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=" C1' G B -45 " pdb=" N9 G B -45 " ideal model delta sigma weight residual 1.475 1.455 0.020 1.50e-02 4.44e+03 1.78e+00 bond pdb=" O5' C B-107 " pdb=" C5' C B-107 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.64e+00 bond pdb=" N9 G B -45 " pdb=" C4 G B -45 " ideal model delta sigma weight residual 1.375 1.400 -0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" CB TRP A 313 " pdb=" CG TRP A 313 " ideal model delta sigma weight residual 1.498 1.461 0.037 3.10e-02 1.04e+03 1.41e+00 bond pdb=" C5 DC D -8 " pdb=" C6 DC D -8 " ideal model delta sigma weight residual 1.337 1.360 -0.023 2.00e-02 2.50e+03 1.37e+00 ... (remaining 6162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 8152 0.85 - 1.71: 663 1.71 - 2.56: 102 2.56 - 3.41: 26 3.41 - 4.27: 9 Bond angle restraints: 8952 Sorted by residual: angle pdb=" N VAL A 346 " pdb=" CA VAL A 346 " pdb=" C VAL A 346 " ideal model delta sigma weight residual 106.21 109.76 -3.55 1.07e+00 8.73e-01 1.10e+01 angle pdb=" O3' C B-107 " pdb=" C3' C B-107 " pdb=" C2' C B-107 " ideal model delta sigma weight residual 113.70 109.43 4.27 1.50e+00 4.44e-01 8.09e+00 angle pdb=" CA TYR A 309 " pdb=" CB TYR A 309 " pdb=" CG TYR A 309 " ideal model delta sigma weight residual 113.90 118.12 -4.22 1.80e+00 3.09e-01 5.49e+00 angle pdb=" C HIS A 34 " pdb=" N PHE A 35 " pdb=" CA PHE A 35 " ideal model delta sigma weight residual 121.14 117.32 3.82 1.75e+00 3.27e-01 4.76e+00 angle pdb=" CA VAL A 346 " pdb=" C VAL A 346 " pdb=" O VAL A 346 " ideal model delta sigma weight residual 122.63 120.76 1.87 8.70e-01 1.32e+00 4.64e+00 ... (remaining 8947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 3010 18.12 - 36.25: 360 36.25 - 54.37: 229 54.37 - 72.49: 140 72.49 - 90.62: 27 Dihedral angle restraints: 3766 sinusoidal: 2717 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 3763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 805 0.033 - 0.067: 201 0.067 - 0.100: 47 0.100 - 0.134: 13 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: 0.030 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: 0.010 Set scattering table: 0.020 Process input model: 8.700 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 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= 0.229 Angle : 0.887 54.546 8958 Z= 0.332 Chirality : 0.034 0.167 1070 Planarity : 0.004 0.044 648 Dihedral : 22.060 90.616 3092 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 covalent geometry : bond 0.00476 ( 6167) covalent geometry : angle 0.53253 ( 8952) hydrogen bonds : bond 0.14264 ( 310) hydrogen bonds : angle 5.30813 ( 727) metal coordination : bond 0.04283 ( 4) metal coordination : angle 27.42998 ( 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 : 0.148 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: 0.1210 time to fit residues: 9.9897 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 : 0.148 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4148 r_free = 0.4148 target = 0.177120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.134716 restraints weight = 8393.272| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.65 r_work: 0.3557 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6171 Z= 0.179 Angle : 0.563 14.419 8958 Z= 0.285 Chirality : 0.035 0.194 1070 Planarity : 0.004 0.046 648 Dihedral : 22.981 94.500 2380 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.87 % Allowed : 12.01 % 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: 2.18 (0.45), residues: 358 helix: 2.40 (0.37), residues: 175 sheet: 0.40 (0.62), residues: 81 loop : 0.78 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 270 TYR 0.020 0.002 TYR A 309 PHE 0.024 0.002 PHE A 35 TRP 0.008 0.001 TRP A 70 HIS 0.005 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 6167) covalent geometry : angle 0.51391 ( 8952) hydrogen bonds : bond 0.05171 ( 310) hydrogen bonds : angle 3.79573 ( 727) metal coordination : bond 0.01288 ( 4) metal coordination : angle 8.88618 ( 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: 15 poor density : 33 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7560 (tp) cc_final: 0.7321 (tt) REVERT: A 48 LYS cc_start: 0.7581 (mmtt) cc_final: 0.6791 (pttt) REVERT: A 121 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: A 205 ARG cc_start: 0.7241 (mtt180) cc_final: 0.6891 (mtm110) REVERT: A 210 GLN cc_start: 0.8792 (pt0) cc_final: 0.8570 (pt0) REVERT: A 278 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6179 (pt0) REVERT: A 338 ASN cc_start: 0.6487 (p0) cc_final: 0.5859 (p0) outliers start: 15 outliers final: 9 residues processed: 47 average time/residue: 0.1078 time to fit residues: 6.2144 Evaluate side-chains 40 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 37 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.172680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133401 restraints weight = 8354.201| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.71 r_work: 0.3487 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 6171 Z= 0.266 Angle : 0.609 7.894 8958 Z= 0.327 Chirality : 0.039 0.248 1070 Planarity : 0.005 0.050 648 Dihedral : 23.092 96.612 2375 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.22 % Allowed : 13.64 % 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: 1.66 (0.45), residues: 358 helix: 1.96 (0.38), residues: 175 sheet: -0.00 (0.64), residues: 75 loop : 0.69 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 39 TYR 0.024 0.002 TYR A 309 PHE 0.028 0.002 PHE A 35 TRP 0.008 0.001 TRP A 70 HIS 0.005 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00573 ( 6167) covalent geometry : angle 0.60006 ( 8952) hydrogen bonds : bond 0.06158 ( 310) hydrogen bonds : angle 3.92892 ( 727) metal coordination : bond 0.00628 ( 4) metal coordination : angle 4.16928 ( 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 47 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7670 (tp) cc_final: 0.7457 (tt) REVERT: A 48 LYS cc_start: 0.7663 (mmtt) cc_final: 0.6817 (pttt) REVERT: A 121 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8079 (mp10) REVERT: A 205 ARG cc_start: 0.7106 (mtt180) cc_final: 0.6873 (mtm110) REVERT: A 278 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6072 (pt0) outliers start: 13 outliers final: 9 residues processed: 47 average time/residue: 0.1058 time to fit residues: 6.2606 Evaluate side-chains 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 10.0000 chunk 45 optimal weight: 40.0000 chunk 36 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.177856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.139080 restraints weight = 8503.447| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.68 r_work: 0.3520 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6171 Z= 0.166 Angle : 0.501 5.049 8958 Z= 0.274 Chirality : 0.034 0.185 1070 Planarity : 0.004 0.049 648 Dihedral : 22.915 96.059 2372 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.90 % Allowed : 13.64 % 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: 1.85 (0.45), residues: 358 helix: 2.22 (0.38), residues: 175 sheet: 0.00 (0.64), residues: 75 loop : 0.66 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 231 TYR 0.022 0.002 TYR A 309 PHE 0.021 0.002 PHE A 35 TRP 0.011 0.001 TRP A 349 HIS 0.004 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6167) covalent geometry : angle 0.49524 ( 8952) hydrogen bonds : bond 0.04728 ( 310) hydrogen bonds : angle 3.57324 ( 727) metal coordination : bond 0.00324 ( 4) metal coordination : angle 3.02114 ( 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 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7587 (tp) cc_final: 0.7363 (tt) REVERT: A 45 GLU cc_start: 0.7012 (tt0) cc_final: 0.6738 (pt0) REVERT: A 48 LYS cc_start: 0.7699 (mmtt) cc_final: 0.6795 (pttt) REVERT: A 121 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7927 (mp10) REVERT: A 205 ARG cc_start: 0.7164 (mtt180) cc_final: 0.6773 (mtm110) REVERT: A 278 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5826 (pt0) REVERT: A 329 GLN cc_start: 0.8200 (mt0) cc_final: 0.7633 (mm-40) outliers start: 12 outliers final: 9 residues processed: 43 average time/residue: 0.0842 time to fit residues: 4.7659 Evaluate side-chains 40 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 3 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.171463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.132273 restraints weight = 8533.250| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.76 r_work: 0.3460 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2546 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= 0.303 Angle : 0.637 5.616 8958 Z= 0.341 Chirality : 0.040 0.254 1070 Planarity : 0.005 0.052 648 Dihedral : 23.133 97.097 2372 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.87 % Allowed : 14.29 % Favored : 80.84 % 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: 1.15 (0.45), residues: 358 helix: 1.69 (0.38), residues: 176 sheet: -0.47 (0.62), residues: 75 loop : 0.33 (0.61), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 39 TYR 0.024 0.003 TYR A 309 PHE 0.025 0.003 PHE A 35 TRP 0.008 0.001 TRP A 141 HIS 0.005 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00656 ( 6167) covalent geometry : angle 0.63131 ( 8952) hydrogen bonds : bond 0.06488 ( 310) hydrogen bonds : angle 3.91438 ( 727) metal coordination : bond 0.00574 ( 4) metal coordination : angle 3.25868 ( 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 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 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7686 (tp) cc_final: 0.7457 (tt) REVERT: A 45 GLU cc_start: 0.7031 (tt0) cc_final: 0.6722 (pt0) REVERT: A 48 LYS cc_start: 0.7652 (mmtt) cc_final: 0.6872 (pttt) REVERT: A 121 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8160 (mp10) REVERT: A 205 ARG cc_start: 0.6921 (mtt180) cc_final: 0.6687 (mtm110) REVERT: A 233 LYS cc_start: 0.7118 (pttt) cc_final: 0.6211 (mmtt) REVERT: A 278 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.5990 (pt0) outliers start: 15 outliers final: 10 residues processed: 44 average time/residue: 0.0811 time to fit residues: 4.6645 Evaluate side-chains 41 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 0.0030 chunk 30 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.176153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136694 restraints weight = 8478.590| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.66 r_work: 0.3532 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6171 Z= 0.149 Angle : 0.486 4.806 8958 Z= 0.266 Chirality : 0.033 0.177 1070 Planarity : 0.004 0.050 648 Dihedral : 22.949 96.190 2371 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.87 % Allowed : 13.96 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.45), residues: 358 helix: 2.17 (0.38), residues: 176 sheet: -0.31 (0.62), residues: 75 loop : 0.35 (0.62), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 221 TYR 0.020 0.002 TYR A 309 PHE 0.019 0.002 PHE A 35 TRP 0.010 0.001 TRP A 349 HIS 0.004 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6167) covalent geometry : angle 0.48310 ( 8952) hydrogen bonds : bond 0.04610 ( 310) hydrogen bonds : angle 3.48701 ( 727) metal coordination : bond 0.00232 ( 4) metal coordination : angle 2.22307 ( 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 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.6942 (OUTLIER) cc_final: 0.6557 (p0) REVERT: A 45 GLU cc_start: 0.7000 (tt0) cc_final: 0.6753 (pt0) REVERT: A 48 LYS cc_start: 0.7384 (mmtt) cc_final: 0.6713 (pttt) REVERT: A 121 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7890 (mp10) REVERT: A 205 ARG cc_start: 0.7132 (mtt180) cc_final: 0.6704 (mtm110) REVERT: A 329 GLN cc_start: 0.8149 (mt0) cc_final: 0.7303 (mm-40) outliers start: 15 outliers final: 12 residues processed: 43 average time/residue: 0.0876 time to fit residues: 4.9239 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 : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN 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 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 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: 9.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.178139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.142281 restraints weight = 8839.307| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.78 r_work: 0.3484 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 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 : 0.003 0.041 6171 Z= 0.124 Angle : 0.445 4.766 8958 Z= 0.246 Chirality : 0.031 0.140 1070 Planarity : 0.003 0.049 648 Dihedral : 22.774 95.225 2371 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 2.08 (0.46), residues: 358 helix: 2.67 (0.38), residues: 175 sheet: -0.07 (0.63), residues: 73 loop : 0.38 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 110 TYR 0.019 0.001 TYR A 309 PHE 0.014 0.001 PHE A 35 TRP 0.010 0.001 TRP A 349 HIS 0.003 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6167) covalent geometry : angle 0.44311 ( 8952) hydrogen bonds : bond 0.04221 ( 310) hydrogen bonds : angle 3.31296 ( 727) metal coordination : bond 0.00139 ( 4) metal coordination : angle 1.76701 ( 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 46 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 30 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7384 (mmtt) cc_final: 0.6670 (pttt) REVERT: A 121 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7806 (mp10) REVERT: A 205 ARG cc_start: 0.7268 (mtt180) cc_final: 0.7067 (mtm110) REVERT: A 278 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6110 (pt0) REVERT: A 329 GLN cc_start: 0.8215 (mt0) cc_final: 0.7684 (mm-40) outliers start: 16 outliers final: 13 residues processed: 46 average time/residue: 0.0758 time to fit residues: 4.6843 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 : 0.143 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 341 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 30.0000 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 45 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.169964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.132711 restraints weight = 8526.102| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.66 r_work: 0.3423 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 6171 Z= 0.326 Angle : 0.661 6.655 8958 Z= 0.348 Chirality : 0.041 0.251 1070 Planarity : 0.005 0.052 648 Dihedral : 23.068 97.391 2371 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.84 % Allowed : 13.31 % Favored : 80.84 % 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: 0.92 (0.44), residues: 358 helix: 1.66 (0.37), residues: 176 sheet: -0.77 (0.60), residues: 75 loop : 0.09 (0.60), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 38 TYR 0.024 0.003 TYR A 309 PHE 0.025 0.003 PHE A 35 TRP 0.011 0.001 TRP A 141 HIS 0.005 0.002 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00706 ( 6167) covalent geometry : angle 0.64988 ( 8952) hydrogen bonds : bond 0.06631 ( 310) hydrogen bonds : angle 3.90476 ( 727) metal coordination : bond 0.00547 ( 4) metal coordination : angle 4.73165 ( 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 47 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 29 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7595 (OUTLIER) cc_final: 0.7392 (p0) REVERT: A 48 LYS cc_start: 0.7566 (mmtt) cc_final: 0.6982 (pttt) REVERT: A 121 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8047 (mp10) REVERT: A 205 ARG cc_start: 0.7099 (mtt180) cc_final: 0.6761 (mtm110) REVERT: A 233 LYS cc_start: 0.7121 (pttt) cc_final: 0.6224 (mmtt) REVERT: A 278 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6051 (pt0) REVERT: A 329 GLN cc_start: 0.8259 (mt0) cc_final: 0.7510 (mm-40) outliers start: 18 outliers final: 13 residues processed: 46 average time/residue: 0.0821 time to fit residues: 5.0031 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 : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 58 GLU 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 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 Chi-restraints excluded: chain A residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 30.0000 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.175082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139291 restraints weight = 8689.715| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.64 r_work: 0.3481 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6171 Z= 0.151 Angle : 0.502 7.566 8958 Z= 0.268 Chirality : 0.033 0.167 1070 Planarity : 0.004 0.051 648 Dihedral : 22.870 96.249 2371 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.87 % Allowed : 14.61 % Favored : 80.52 % 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: 1.52 (0.46), residues: 358 helix: 2.23 (0.38), residues: 176 sheet: -0.53 (0.62), residues: 75 loop : 0.24 (0.64), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.020 0.002 TYR A 309 PHE 0.019 0.002 PHE A 35 TRP 0.011 0.001 TRP A 349 HIS 0.003 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6167) covalent geometry : angle 0.49291 ( 8952) hydrogen bonds : bond 0.04583 ( 310) hydrogen bonds : angle 3.46377 ( 727) metal coordination : bond 0.00298 ( 4) metal coordination : angle 3.62027 ( 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 42 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 27 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7368 (mmtt) cc_final: 0.6903 (pttt) REVERT: A 121 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: A 278 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6195 (pt0) REVERT: A 329 GLN cc_start: 0.8398 (mt0) cc_final: 0.7659 (mm-40) outliers start: 15 outliers final: 11 residues processed: 42 average time/residue: 0.0741 time to fit residues: 4.2114 Evaluate side-chains 38 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 58 GLU 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 121 GLN 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 Chi-restraints excluded: chain A residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 42 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.176039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137957 restraints weight = 8773.956| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.92 r_work: 0.3542 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6171 Z= 0.187 Angle : 0.528 5.190 8958 Z= 0.283 Chirality : 0.035 0.194 1070 Planarity : 0.004 0.052 648 Dihedral : 22.887 96.654 2370 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.87 % Allowed : 13.96 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.46), residues: 358 helix: 2.19 (0.38), residues: 176 sheet: -0.46 (0.62), residues: 73 loop : 0.12 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.022 0.002 TYR A 309 PHE 0.023 0.002 PHE A 35 TRP 0.008 0.001 TRP A 349 HIS 0.004 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 6167) covalent geometry : angle 0.52088 ( 8952) hydrogen bonds : bond 0.05115 ( 310) hydrogen bonds : angle 3.54010 ( 727) metal coordination : bond 0.00346 ( 4) metal coordination : angle 3.35529 ( 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 39 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 24 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7434 (mmtt) cc_final: 0.6801 (pttt) REVERT: A 121 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7934 (mp10) REVERT: A 278 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.5861 (pt0) REVERT: A 329 GLN cc_start: 0.8380 (mt0) cc_final: 0.7553 (mm-40) outliers start: 15 outliers final: 13 residues processed: 39 average time/residue: 0.0831 time to fit residues: 4.2555 Evaluate side-chains 39 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 24 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 58 GLU 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 121 GLN 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 Chi-restraints excluded: chain A residue 341 VAL 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: 4.9990 chunk 48 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 31 optimal weight: 50.0000 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 overall best weight: 5.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.174677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.136107 restraints weight = 8594.486| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.82 r_work: 0.3539 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3025 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= 0.227 Angle : 0.561 5.166 8958 Z= 0.299 Chirality : 0.036 0.205 1070 Planarity : 0.004 0.052 648 Dihedral : 22.923 96.115 2370 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.87 % Allowed : 14.29 % Favored : 80.84 % 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: 1.24 (0.45), residues: 358 helix: 2.03 (0.38), residues: 176 sheet: -0.65 (0.62), residues: 73 loop : 0.02 (0.62), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.022 0.002 TYR A 309 PHE 0.024 0.002 PHE A 35 TRP 0.008 0.002 TRP A 349 HIS 0.004 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 6167) covalent geometry : angle 0.55406 ( 8952) hydrogen bonds : bond 0.05479 ( 310) hydrogen bonds : angle 3.61869 ( 727) metal coordination : bond 0.00414 ( 4) metal coordination : angle 3.35965 ( 6) =============================================================================== Job complete usr+sys time: 1305.85 seconds wall clock time: 23 minutes 2.50 seconds (1382.50 seconds total)