Starting phenix.real_space_refine on Tue Feb 11 16:57:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zao_39882/02_2025/8zao_39882_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zao_39882/02_2025/8zao_39882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zao_39882/02_2025/8zao_39882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zao_39882/02_2025/8zao_39882.map" model { file = "/net/cci-nas-00/data/ceres_data/8zao_39882/02_2025/8zao_39882_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zao_39882/02_2025/8zao_39882_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians K 15 8.98 5 S 60 5.16 5 C 4326 2.51 5 N 966 2.21 5 O 1065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6432 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2109 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "B" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2109 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "C" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2109 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 25 Unusual residues: {' K': 5, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 25 Unusual residues: {' K': 5, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 25 Unusual residues: {' K': 5, 'RET': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 8.13, per 1000 atoms: 1.26 Number of scatterers: 6432 At special positions: 0 Unit cell: (74.9, 73.5, 79.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 15 19.00 S 60 16.00 O 1065 8.00 N 966 7.00 C 4326 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 923.9 milliseconds 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1434 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 73.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 21 through 50 removed outlier: 3.736A pdb=" N GLY A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 68 through 90 Processing helix chain 'A' and resid 105 through 122 removed outlier: 3.740A pdb=" N THR A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 178 removed outlier: 3.823A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Proline residue: A 164 - end of helix removed outlier: 3.616A pdb=" N ARG A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.900A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 208 removed outlier: 3.637A pdb=" N PHE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 50 removed outlier: 3.743A pdb=" N GLY B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 105 through 122 removed outlier: 3.757A pdb=" N THR B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 178 removed outlier: 3.822A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Proline residue: B 164 - end of helix removed outlier: 3.588A pdb=" N ARG B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 199 removed outlier: 3.907A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 removed outlier: 3.597A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 50 removed outlier: 3.743A pdb=" N GLY C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 105 through 122 removed outlier: 3.711A pdb=" N THR C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 178 removed outlier: 3.821A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Proline residue: C 164 - end of helix removed outlier: 3.619A pdb=" N ARG C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 199 removed outlier: 3.900A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 208 removed outlier: 3.632A pdb=" N PHE C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 414 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1814 1.35 - 1.46: 1976 1.46 - 1.58: 2768 1.58 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 6639 Sorted by residual: bond pdb=" C TRP B 199 " pdb=" N PRO B 200 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.19e-02 7.06e+03 2.64e+00 bond pdb=" C TRP A 199 " pdb=" N PRO A 200 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.19e-02 7.06e+03 2.31e+00 bond pdb=" C TRP C 199 " pdb=" N PRO C 200 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.19e-02 7.06e+03 2.24e+00 bond pdb=" CA PHE C 202 " pdb=" C PHE C 202 " ideal model delta sigma weight residual 1.520 1.532 -0.011 1.23e-02 6.61e+03 8.32e-01 bond pdb=" C PHE A 198 " pdb=" N TRP A 199 " ideal model delta sigma weight residual 1.332 1.344 -0.012 1.33e-02 5.65e+03 7.74e-01 ... (remaining 6634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 8835 1.59 - 3.17: 184 3.17 - 4.76: 14 4.76 - 6.35: 12 6.35 - 7.93: 3 Bond angle restraints: 9048 Sorted by residual: angle pdb=" C GLY A 93 " pdb=" N THR A 94 " pdb=" CA THR A 94 " ideal model delta sigma weight residual 120.49 128.42 -7.93 1.42e+00 4.96e-01 3.12e+01 angle pdb=" C GLY B 93 " pdb=" N THR B 94 " pdb=" CA THR B 94 " ideal model delta sigma weight residual 120.49 128.40 -7.91 1.42e+00 4.96e-01 3.11e+01 angle pdb=" C GLY C 93 " pdb=" N THR C 94 " pdb=" CA THR C 94 " ideal model delta sigma weight residual 120.49 128.40 -7.91 1.42e+00 4.96e-01 3.10e+01 angle pdb=" C TRP B 102 " pdb=" N TYR B 103 " pdb=" CA TYR B 103 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.99e+00 angle pdb=" C TRP C 102 " pdb=" N TYR C 103 " pdb=" CA TYR C 103 " ideal model delta sigma weight residual 121.54 126.16 -4.62 1.91e+00 2.74e-01 5.86e+00 ... (remaining 9043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3266 17.99 - 35.99: 337 35.99 - 53.98: 87 53.98 - 71.97: 12 71.97 - 89.97: 3 Dihedral angle restraints: 3705 sinusoidal: 1449 harmonic: 2256 Sorted by residual: dihedral pdb=" N ARG A 244 " pdb=" CA ARG A 244 " pdb=" CB ARG A 244 " pdb=" CG ARG A 244 " ideal model delta sinusoidal sigma weight residual -180.00 -120.20 -59.80 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG C 244 " pdb=" CA ARG C 244 " pdb=" CB ARG C 244 " pdb=" CG ARG C 244 " ideal model delta sinusoidal sigma weight residual -180.00 -120.32 -59.68 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLU C 252 " pdb=" CB GLU C 252 " pdb=" CG GLU C 252 " pdb=" CD GLU C 252 " ideal model delta sinusoidal sigma weight residual -60.00 -119.58 59.58 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 477 0.024 - 0.047: 266 0.047 - 0.071: 121 0.071 - 0.095: 41 0.095 - 0.119: 22 Chirality restraints: 927 Sorted by residual: chirality pdb=" CA TYR A 103 " pdb=" N TYR A 103 " pdb=" C TYR A 103 " pdb=" CB TYR A 103 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA TYR C 103 " pdb=" N TYR C 103 " pdb=" C TYR C 103 " pdb=" CB TYR C 103 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA TYR B 103 " pdb=" N TYR B 103 " pdb=" C TYR B 103 " pdb=" CB TYR B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.35e-01 ... (remaining 924 not shown) Planarity restraints: 1113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 199 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO C 200 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 199 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO B 200 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 199 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A 200 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " 0.032 5.00e-02 4.00e+02 ... (remaining 1110 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.31: 22 2.31 - 3.02: 3718 3.02 - 3.72: 12654 3.72 - 4.43: 21002 4.43 - 5.14: 33112 Nonbonded interactions: 70508 Sorted by model distance: nonbonded pdb=" K K C 302 " pdb=" O HOH C 407 " model vdw 1.601 2.850 nonbonded pdb=" K K B 302 " pdb=" O HOH B 407 " model vdw 1.602 2.850 nonbonded pdb=" K K A 302 " pdb=" O HOH A 407 " model vdw 1.605 2.850 nonbonded pdb=" K K A 304 " pdb=" O HOH A 404 " model vdw 1.995 2.850 nonbonded pdb=" K K B 302 " pdb=" O HOH B 406 " model vdw 2.024 2.850 ... (remaining 70503 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 29.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.670 Find NCS groups from input model: 0.120 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:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6639 Z= 0.204 Angle : 0.571 7.935 9048 Z= 0.328 Chirality : 0.038 0.119 927 Planarity : 0.006 0.058 1113 Dihedral : 15.637 89.966 2271 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.64 % Allowed : 15.25 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.30), residues: 771 helix: 1.59 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.93 (0.42), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 42 HIS 0.002 0.001 HIS C 225 PHE 0.011 0.001 PHE C 165 TYR 0.011 0.001 TYR B 81 ARG 0.001 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8151 (mmmt) cc_final: 0.7604 (mmmt) REVERT: A 178 LEU cc_start: 0.8150 (mt) cc_final: 0.7799 (mm) REVERT: B 14 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7605 (mmmt) REVERT: B 178 LEU cc_start: 0.8130 (mt) cc_final: 0.7774 (mm) REVERT: B 230 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7587 (tp) REVERT: C 14 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7624 (mmmt) REVERT: C 178 LEU cc_start: 0.8170 (mt) cc_final: 0.7787 (mm) outliers start: 11 outliers final: 8 residues processed: 81 average time/residue: 0.8100 time to fit residues: 71.2746 Evaluate side-chains 79 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 233 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3237 r_free = 0.3237 target = 0.106309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.093595 restraints weight = 7185.078| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.50 r_work: 0.3027 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6639 Z= 0.262 Angle : 0.530 5.518 9048 Z= 0.267 Chirality : 0.039 0.128 927 Planarity : 0.005 0.041 1113 Dihedral : 8.817 89.843 901 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 3.29 % Allowed : 14.20 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.30), residues: 771 helix: 1.75 (0.21), residues: 528 sheet: None (None), residues: 0 loop : 1.02 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 42 HIS 0.002 0.001 HIS C 225 PHE 0.020 0.001 PHE A 144 TYR 0.010 0.002 TYR A 81 ARG 0.001 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7594 (mmmt) REVERT: A 201 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7355 (mtt) REVERT: A 252 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7635 (mm-30) REVERT: B 14 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7612 (mptt) REVERT: B 183 LYS cc_start: 0.7370 (mtpp) cc_final: 0.7091 (tppp) REVERT: B 201 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7280 (mtt) REVERT: B 230 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7379 (tp) REVERT: B 252 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7747 (mm-30) REVERT: C 14 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7587 (mmmt) REVERT: C 252 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7608 (mm-30) outliers start: 22 outliers final: 10 residues processed: 100 average time/residue: 0.8527 time to fit residues: 91.4925 Evaluate side-chains 91 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.104886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.092257 restraints weight = 7185.833| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.50 r_work: 0.2993 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6639 Z= 0.272 Angle : 0.523 5.508 9048 Z= 0.258 Chirality : 0.039 0.125 927 Planarity : 0.005 0.038 1113 Dihedral : 8.714 88.464 899 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.59 % Allowed : 14.95 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.29), residues: 771 helix: 1.66 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 0.87 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 42 HIS 0.003 0.001 HIS C 215 PHE 0.025 0.001 PHE A 144 TYR 0.009 0.001 TYR C 180 ARG 0.001 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7651 (mptt) REVERT: A 183 LYS cc_start: 0.7428 (mtpp) cc_final: 0.7141 (tppp) REVERT: A 252 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7652 (mm-30) REVERT: B 14 LYS cc_start: 0.8152 (mmmt) cc_final: 0.7649 (mptt) REVERT: B 183 LYS cc_start: 0.7405 (mtpp) cc_final: 0.7134 (tppp) REVERT: B 230 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7449 (tp) REVERT: B 252 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7793 (mm-30) REVERT: C 14 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7627 (mmmt) REVERT: C 183 LYS cc_start: 0.7455 (mtpp) cc_final: 0.7161 (tppp) REVERT: C 252 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7661 (mm-30) outliers start: 24 outliers final: 10 residues processed: 92 average time/residue: 0.9993 time to fit residues: 98.0777 Evaluate side-chains 88 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.107462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094539 restraints weight = 7143.882| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.51 r_work: 0.3004 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6639 Z= 0.195 Angle : 0.483 5.508 9048 Z= 0.240 Chirality : 0.037 0.115 927 Planarity : 0.005 0.039 1113 Dihedral : 8.673 89.073 899 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.59 % Allowed : 15.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.29), residues: 771 helix: 1.80 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 0.89 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 42 HIS 0.002 0.001 HIS C 215 PHE 0.019 0.001 PHE C 144 TYR 0.007 0.001 TYR B 81 ARG 0.001 0.000 ARG C 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8119 (mmmt) cc_final: 0.7594 (mptt) REVERT: A 183 LYS cc_start: 0.7287 (mtpp) cc_final: 0.7033 (tppp) REVERT: A 252 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7649 (mm-30) REVERT: B 14 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7591 (mptt) REVERT: B 178 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7806 (mm) REVERT: B 183 LYS cc_start: 0.7262 (mtpp) cc_final: 0.7017 (tppp) REVERT: B 230 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7341 (tp) REVERT: B 252 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: C 14 LYS cc_start: 0.8140 (mmmt) cc_final: 0.7558 (mmmt) REVERT: C 178 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7758 (mm) REVERT: C 183 LYS cc_start: 0.7307 (mtpp) cc_final: 0.7044 (tppp) REVERT: C 252 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7681 (mm-30) outliers start: 24 outliers final: 10 residues processed: 99 average time/residue: 0.9464 time to fit residues: 99.8721 Evaluate side-chains 89 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.106982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.094061 restraints weight = 7103.829| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.51 r_work: 0.2964 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6639 Z= 0.223 Angle : 0.498 5.534 9048 Z= 0.245 Chirality : 0.038 0.119 927 Planarity : 0.005 0.038 1113 Dihedral : 8.647 88.432 899 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.74 % Allowed : 15.70 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.29), residues: 771 helix: 1.82 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 0.89 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 42 HIS 0.002 0.001 HIS C 215 PHE 0.020 0.001 PHE A 144 TYR 0.008 0.001 TYR A 180 ARG 0.001 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7498 (mmmt) REVERT: A 183 LYS cc_start: 0.7213 (mtpp) cc_final: 0.6968 (tppp) REVERT: A 252 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7619 (mm-30) REVERT: B 14 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7559 (mptt) REVERT: B 178 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7760 (mm) REVERT: B 183 LYS cc_start: 0.7169 (mtpp) cc_final: 0.6939 (tppp) REVERT: B 230 LEU cc_start: 0.7490 (tp) cc_final: 0.7271 (tp) REVERT: B 252 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7729 (mm-30) REVERT: C 14 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7526 (mmmt) REVERT: C 178 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7701 (mm) REVERT: C 183 LYS cc_start: 0.7211 (mtpp) cc_final: 0.6954 (tppp) REVERT: C 252 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7653 (mm-30) outliers start: 25 outliers final: 10 residues processed: 91 average time/residue: 0.9552 time to fit residues: 92.6997 Evaluate side-chains 87 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 68 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3227 r_free = 0.3227 target = 0.106310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.093374 restraints weight = 7141.341| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.50 r_work: 0.2994 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6639 Z= 0.199 Angle : 0.485 5.517 9048 Z= 0.240 Chirality : 0.038 0.115 927 Planarity : 0.005 0.038 1113 Dihedral : 8.463 85.985 897 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.04 % Allowed : 15.70 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.29), residues: 771 helix: 1.85 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.97 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 42 HIS 0.002 0.001 HIS C 215 PHE 0.022 0.001 PHE B 144 TYR 0.008 0.001 TYR B 81 ARG 0.001 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7539 (mmmt) REVERT: A 178 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7773 (mm) REVERT: A 183 LYS cc_start: 0.7306 (mtpp) cc_final: 0.7079 (tppp) REVERT: A 252 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7659 (mm-30) REVERT: B 14 LYS cc_start: 0.8116 (mmmt) cc_final: 0.7584 (mptt) REVERT: B 178 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7819 (mm) REVERT: B 183 LYS cc_start: 0.7262 (mtpp) cc_final: 0.7043 (tppp) REVERT: B 230 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7380 (tp) REVERT: B 252 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: C 14 LYS cc_start: 0.8152 (mmmt) cc_final: 0.7574 (mmmt) REVERT: C 178 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7755 (mm) REVERT: C 183 LYS cc_start: 0.7325 (mtpp) cc_final: 0.7074 (tppp) REVERT: C 252 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7689 (mm-30) outliers start: 27 outliers final: 10 residues processed: 92 average time/residue: 0.9420 time to fit residues: 92.6775 Evaluate side-chains 85 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 0.0370 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.105357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.092386 restraints weight = 7118.662| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.51 r_work: 0.3002 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6639 Z= 0.229 Angle : 0.504 5.530 9048 Z= 0.249 Chirality : 0.038 0.121 927 Planarity : 0.005 0.039 1113 Dihedral : 8.463 83.151 897 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.59 % Allowed : 15.84 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.29), residues: 771 helix: 1.88 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 1.12 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 42 HIS 0.003 0.001 HIS C 215 PHE 0.023 0.001 PHE B 144 TYR 0.010 0.001 TYR B 103 ARG 0.001 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8141 (mmmt) cc_final: 0.7566 (mmmt) REVERT: A 178 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7798 (mm) REVERT: A 183 LYS cc_start: 0.7372 (mtpp) cc_final: 0.7142 (tppp) REVERT: A 252 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7661 (mm-30) REVERT: B 14 LYS cc_start: 0.8144 (mmmt) cc_final: 0.7621 (mptt) REVERT: B 178 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7851 (mm) REVERT: B 183 LYS cc_start: 0.7316 (mtpp) cc_final: 0.7102 (tppp) REVERT: B 230 LEU cc_start: 0.7654 (tp) cc_final: 0.7434 (tp) REVERT: B 252 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: C 14 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7607 (mmmt) REVERT: C 178 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7798 (mm) REVERT: C 183 LYS cc_start: 0.7376 (mtpp) cc_final: 0.7126 (tppp) REVERT: C 252 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7706 (mm-30) outliers start: 24 outliers final: 11 residues processed: 90 average time/residue: 0.9242 time to fit residues: 89.0147 Evaluate side-chains 85 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.107049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.094156 restraints weight = 7111.071| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.50 r_work: 0.2995 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6639 Z= 0.252 Angle : 0.516 5.551 9048 Z= 0.255 Chirality : 0.039 0.128 927 Planarity : 0.005 0.041 1113 Dihedral : 8.500 82.652 897 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.19 % Allowed : 14.80 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.29), residues: 771 helix: 1.87 (0.21), residues: 534 sheet: None (None), residues: 0 loop : 1.05 (0.44), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 42 HIS 0.003 0.001 HIS C 215 PHE 0.021 0.001 PHE B 144 TYR 0.009 0.001 TYR C 180 ARG 0.001 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8142 (mmmt) cc_final: 0.7572 (mmmt) REVERT: A 183 LYS cc_start: 0.7391 (mtpp) cc_final: 0.7155 (tppp) REVERT: A 252 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: B 14 LYS cc_start: 0.8144 (mmmt) cc_final: 0.7630 (mptt) REVERT: B 178 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7860 (mm) REVERT: B 183 LYS cc_start: 0.7336 (mtpp) cc_final: 0.7115 (tppp) REVERT: B 230 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7461 (tp) REVERT: B 252 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7728 (mm-30) REVERT: C 14 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7621 (mmmt) REVERT: C 178 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7801 (mm) REVERT: C 183 LYS cc_start: 0.7391 (mtpp) cc_final: 0.7137 (tppp) REVERT: C 252 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7709 (mm-30) outliers start: 28 outliers final: 12 residues processed: 93 average time/residue: 0.9686 time to fit residues: 96.1225 Evaluate side-chains 89 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.105911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.092903 restraints weight = 7194.106| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.52 r_work: 0.2988 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6639 Z= 0.204 Angle : 0.500 5.521 9048 Z= 0.249 Chirality : 0.038 0.143 927 Planarity : 0.005 0.041 1113 Dihedral : 8.473 80.437 897 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.69 % Allowed : 16.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.29), residues: 771 helix: 1.92 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 1.17 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 42 HIS 0.002 0.001 HIS A 215 PHE 0.019 0.001 PHE A 144 TYR 0.011 0.001 TYR A 103 ARG 0.001 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8126 (mmmt) cc_final: 0.7558 (mmmt) REVERT: A 178 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7779 (mm) REVERT: A 183 LYS cc_start: 0.7302 (mtpp) cc_final: 0.7076 (tppp) REVERT: A 252 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: B 14 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7597 (mptt) REVERT: B 178 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7819 (mm) REVERT: B 183 LYS cc_start: 0.7267 (mtpp) cc_final: 0.7055 (tppp) REVERT: B 230 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7410 (tp) REVERT: B 252 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7721 (mm-30) REVERT: C 14 LYS cc_start: 0.8165 (mmmt) cc_final: 0.7595 (mmmt) REVERT: C 178 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7757 (mm) REVERT: C 183 LYS cc_start: 0.7317 (mtpp) cc_final: 0.7074 (tppp) REVERT: C 252 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7698 (mm-30) outliers start: 18 outliers final: 9 residues processed: 85 average time/residue: 0.9616 time to fit residues: 87.2239 Evaluate side-chains 83 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 9 optimal weight: 0.0570 chunk 47 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.108705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.095811 restraints weight = 7078.524| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.50 r_work: 0.3004 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6639 Z= 0.189 Angle : 0.490 5.505 9048 Z= 0.245 Chirality : 0.038 0.144 927 Planarity : 0.005 0.040 1113 Dihedral : 8.446 78.332 897 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.69 % Allowed : 15.99 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.29), residues: 771 helix: 1.97 (0.21), residues: 537 sheet: None (None), residues: 0 loop : 1.16 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 42 HIS 0.002 0.001 HIS C 215 PHE 0.015 0.001 PHE A 144 TYR 0.007 0.001 TYR C 45 ARG 0.001 0.000 ARG A 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7532 (mmmt) REVERT: A 178 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7763 (mm) REVERT: A 183 LYS cc_start: 0.7252 (mtpp) cc_final: 0.7041 (tppp) REVERT: A 252 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: B 14 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7612 (mptt) REVERT: B 178 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7793 (mm) REVERT: B 252 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7712 (mm-30) REVERT: C 14 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7575 (mmmt) REVERT: C 178 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7745 (mm) REVERT: C 183 LYS cc_start: 0.7286 (mtpp) cc_final: 0.7053 (tppp) REVERT: C 252 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7689 (mt-10) outliers start: 18 outliers final: 8 residues processed: 90 average time/residue: 1.0377 time to fit residues: 99.2571 Evaluate side-chains 82 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.095014 restraints weight = 7189.435| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.52 r_work: 0.3001 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6639 Z= 0.246 Angle : 0.520 5.553 9048 Z= 0.260 Chirality : 0.040 0.163 927 Planarity : 0.005 0.040 1113 Dihedral : 8.306 78.547 897 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.69 % Allowed : 15.84 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.29), residues: 771 helix: 1.91 (0.21), residues: 534 sheet: None (None), residues: 0 loop : 1.03 (0.44), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 42 HIS 0.003 0.001 HIS A 215 PHE 0.022 0.001 PHE A 144 TYR 0.009 0.001 TYR B 180 ARG 0.001 0.000 ARG B 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5403.13 seconds wall clock time: 97 minutes 33.69 seconds (5853.69 seconds total)