Starting phenix.real_space_refine on Tue Sep 24 14:22:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/09_2024/7cr1_30444_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/09_2024/7cr1_30444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/09_2024/7cr1_30444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/09_2024/7cr1_30444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/09_2024/7cr1_30444_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr1_30444/09_2024/7cr1_30444_trim.cif" } resolution = 3.4 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= 0.004 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 S 36 5.16 5 Cl 4 4.86 5 C 5464 2.51 5 N 1384 2.21 5 O 1328 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8220 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2038 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 4, 'TRANS': 245} Chain breaks: 1 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'GB9': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 3.98, per 1000 atoms: 0.48 Number of scatterers: 8220 At special positions: 0 Unit cell: (124.722, 124.722, 75.036, 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) Cl 4 17.00 S 36 16.00 F 4 9.00 O 1328 8.00 N 1384 7.00 C 5464 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 85.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 91 through 115 removed outlier: 4.155A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 147 Processing helix chain 'A' and resid 148 through 151 removed outlier: 3.979A pdb=" N CYS A 151 " --> pdb=" O ALA A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 151' Processing helix chain 'A' and resid 157 through 165 Processing helix chain 'A' and resid 166 through 183 Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.667A pdb=" N MET A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 255 Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.645A pdb=" N THR A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.805A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 329 removed outlier: 3.827A pdb=" N GLY A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 91 through 115 removed outlier: 4.154A pdb=" N TYR B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 147 Processing helix chain 'B' and resid 148 through 151 removed outlier: 3.979A pdb=" N CYS B 151 " --> pdb=" O ALA B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 151' Processing helix chain 'B' and resid 157 through 165 Processing helix chain 'B' and resid 166 through 183 Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.667A pdb=" N MET B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 255 Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.645A pdb=" N THR B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 306 removed outlier: 3.806A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 329 removed outlier: 3.826A pdb=" N GLY B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 91 through 115 removed outlier: 4.154A pdb=" N TYR C 95 " --> pdb=" O TRP C 91 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 147 Processing helix chain 'C' and resid 148 through 151 removed outlier: 3.978A pdb=" N CYS C 151 " --> pdb=" O ALA C 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 148 through 151' Processing helix chain 'C' and resid 157 through 165 Processing helix chain 'C' and resid 166 through 183 Processing helix chain 'C' and resid 196 through 211 removed outlier: 3.666A pdb=" N MET C 208 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 209 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET C 211 " --> pdb=" O ARG C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 228 Processing helix chain 'C' and resid 228 through 255 Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.645A pdb=" N THR C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 306 removed outlier: 3.806A pdb=" N THR C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 329 removed outlier: 3.826A pdb=" N GLY C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 91 through 115 removed outlier: 4.154A pdb=" N TYR D 95 " --> pdb=" O TRP D 91 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 147 Processing helix chain 'D' and resid 148 through 151 removed outlier: 3.978A pdb=" N CYS D 151 " --> pdb=" O ALA D 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 148 through 151' Processing helix chain 'D' and resid 157 through 165 Processing helix chain 'D' and resid 166 through 183 Processing helix chain 'D' and resid 196 through 211 removed outlier: 3.667A pdb=" N MET D 208 " --> pdb=" O GLN D 204 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 255 Processing helix chain 'D' and resid 263 through 276 removed outlier: 3.645A pdb=" N THR D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 306 removed outlier: 3.806A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 329 removed outlier: 3.826A pdb=" N GLY D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1875 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: 2.05 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1184 1.31 - 1.43: 2633 1.43 - 1.56: 4579 1.56 - 1.68: 0 1.68 - 1.81: 52 Bond restraints: 8448 Sorted by residual: bond pdb=" C12 GB9 D 801 " pdb=" N2 GB9 D 801 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" C12 GB9 C 801 " pdb=" N2 GB9 C 801 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" C12 GB9 B 801 " pdb=" N2 GB9 B 801 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" C12 GB9 A 801 " pdb=" N2 GB9 A 801 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" C5 GB9 C 801 " pdb=" C8 GB9 C 801 " ideal model delta sigma weight residual 1.386 1.524 -0.138 2.00e-02 2.50e+03 4.77e+01 ... (remaining 8443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 10693 1.35 - 2.70: 593 2.70 - 4.04: 112 4.04 - 5.39: 29 5.39 - 6.74: 9 Bond angle restraints: 11436 Sorted by residual: angle pdb=" N ASN D 258 " pdb=" CA ASN D 258 " pdb=" C ASN D 258 " ideal model delta sigma weight residual 109.07 114.91 -5.84 1.61e+00 3.86e-01 1.32e+01 angle pdb=" N GLU A 257 " pdb=" CA GLU A 257 " pdb=" C GLU A 257 " ideal model delta sigma weight residual 111.36 115.28 -3.92 1.09e+00 8.42e-01 1.29e+01 angle pdb=" N ASN B 258 " pdb=" CA ASN B 258 " pdb=" C ASN B 258 " ideal model delta sigma weight residual 109.07 114.86 -5.79 1.61e+00 3.86e-01 1.29e+01 angle pdb=" N ASN C 258 " pdb=" CA ASN C 258 " pdb=" C ASN C 258 " ideal model delta sigma weight residual 109.07 114.86 -5.79 1.61e+00 3.86e-01 1.29e+01 angle pdb=" N GLU C 257 " pdb=" CA GLU C 257 " pdb=" C GLU C 257 " ideal model delta sigma weight residual 111.36 115.28 -3.92 1.09e+00 8.42e-01 1.29e+01 ... (remaining 11431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4188 17.35 - 34.69: 456 34.69 - 52.04: 92 52.04 - 69.38: 20 69.38 - 86.73: 16 Dihedral angle restraints: 4772 sinusoidal: 1876 harmonic: 2896 Sorted by residual: dihedral pdb=" CA ARG D 153 " pdb=" C ARG D 153 " pdb=" N TYR D 154 " pdb=" CA TYR D 154 " ideal model delta harmonic sigma weight residual -180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ARG A 153 " pdb=" C ARG A 153 " pdb=" N TYR A 154 " pdb=" CA TYR A 154 " ideal model delta harmonic sigma weight residual -180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ARG B 153 " pdb=" C ARG B 153 " pdb=" N TYR B 154 " pdb=" CA TYR B 154 " ideal model delta harmonic sigma weight residual -180.00 -162.83 -17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 4769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 658 0.030 - 0.060: 397 0.060 - 0.090: 151 0.090 - 0.120: 24 0.120 - 0.150: 18 Chirality restraints: 1248 Sorted by residual: chirality pdb=" CA GLU C 254 " pdb=" N GLU C 254 " pdb=" C GLU C 254 " pdb=" CB GLU C 254 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA GLU D 254 " pdb=" N GLU D 254 " pdb=" C GLU D 254 " pdb=" CB GLU D 254 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA GLU B 254 " pdb=" N GLU B 254 " pdb=" C GLU B 254 " pdb=" CB GLU B 254 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1245 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 284 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO D 285 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 285 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 285 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 284 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO C 285 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 285 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 285 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 284 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 285 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.018 5.00e-02 4.00e+02 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 974 2.73 - 3.27: 8897 3.27 - 3.81: 13274 3.81 - 4.36: 15434 4.36 - 4.90: 26126 Nonbonded interactions: 64705 Sorted by model distance: nonbonded pdb=" O THR B 276 " pdb=" OG1 THR B 277 " model vdw 2.185 3.040 nonbonded pdb=" O THR A 276 " pdb=" OG1 THR A 277 " model vdw 2.185 3.040 nonbonded pdb=" O THR C 276 " pdb=" OG1 THR C 277 " model vdw 2.185 3.040 nonbonded pdb=" O THR D 276 " pdb=" OG1 THR D 277 " model vdw 2.186 3.040 nonbonded pdb=" OE1 GLU C 254 " pdb=" N GLN C 286 " model vdw 2.202 3.120 ... (remaining 64700 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 19.840 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 : 0.012 0.175 8448 Z= 0.807 Angle : 0.735 6.741 11436 Z= 0.413 Chirality : 0.043 0.150 1248 Planarity : 0.003 0.033 1384 Dihedral : 14.924 86.731 2924 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 26.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.00 (0.24), residues: 984 helix: -0.93 (0.15), residues: 808 sheet: None (None), residues: 0 loop : -2.41 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 269 HIS 0.002 0.001 HIS C 324 PHE 0.020 0.002 PHE C 142 TYR 0.012 0.002 TYR B 154 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 0.907 Fit side-chains REVERT: A 76 LYS cc_start: 0.6962 (ptmt) cc_final: 0.6505 (ptmm) REVERT: A 204 GLN cc_start: 0.8762 (mm110) cc_final: 0.8499 (mm110) REVERT: B 76 LYS cc_start: 0.6951 (ptmt) cc_final: 0.6472 (ptmm) REVERT: B 204 GLN cc_start: 0.8757 (mm110) cc_final: 0.8481 (mm110) REVERT: C 204 GLN cc_start: 0.8771 (mm110) cc_final: 0.8491 (mm110) REVERT: D 144 ARG cc_start: 0.6476 (mtt-85) cc_final: 0.6274 (mtt-85) REVERT: D 204 GLN cc_start: 0.8764 (mm110) cc_final: 0.8469 (mm110) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2570 time to fit residues: 70.6927 Evaluate side-chains 189 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 0.0050 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 204 GLN C 204 GLN D 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8448 Z= 0.222 Angle : 0.574 5.758 11436 Z= 0.299 Chirality : 0.039 0.149 1248 Planarity : 0.004 0.037 1384 Dihedral : 4.109 14.642 1124 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.03 % Allowed : 15.07 % Favored : 82.89 % 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: 0.75 (0.26), residues: 984 helix: 1.21 (0.17), residues: 828 sheet: None (None), residues: 0 loop : -3.36 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 146 HIS 0.002 0.001 HIS C 328 PHE 0.008 0.001 PHE C 80 TYR 0.016 0.001 TYR B 74 ARG 0.006 0.001 ARG C 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 0.862 Fit side-chains REVERT: A 89 ARG cc_start: 0.6419 (ptp-110) cc_final: 0.5367 (ptt-90) REVERT: A 101 LEU cc_start: 0.8839 (mt) cc_final: 0.8569 (tt) REVERT: A 326 GLN cc_start: 0.6653 (mt0) cc_final: 0.6431 (tt0) REVERT: B 89 ARG cc_start: 0.6430 (ptp-110) cc_final: 0.5359 (ptt-90) REVERT: B 326 GLN cc_start: 0.6569 (mt0) cc_final: 0.6326 (tt0) REVERT: C 89 ARG cc_start: 0.6354 (ptp-110) cc_final: 0.5303 (ptt-90) REVERT: C 101 LEU cc_start: 0.8818 (mt) cc_final: 0.8547 (tt) REVERT: D 89 ARG cc_start: 0.6301 (ptp-110) cc_final: 0.5279 (ptt-90) REVERT: D 101 LEU cc_start: 0.8806 (mt) cc_final: 0.8538 (tt) outliers start: 17 outliers final: 12 residues processed: 196 average time/residue: 0.2323 time to fit residues: 59.1727 Evaluate side-chains 184 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 172 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 118 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 118 TYR Chi-restraints excluded: chain D residue 171 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN B 323 GLN C 204 GLN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8448 Z= 0.252 Angle : 0.553 6.300 11436 Z= 0.292 Chirality : 0.038 0.151 1248 Planarity : 0.004 0.032 1384 Dihedral : 3.897 13.553 1124 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.47 % Allowed : 17.94 % Favored : 78.59 % 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: 1.58 (0.26), residues: 984 helix: 1.85 (0.17), residues: 812 sheet: None (None), residues: 0 loop : -2.99 (0.44), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.002 0.001 HIS D 328 PHE 0.014 0.001 PHE D 168 TYR 0.010 0.001 TYR A 74 ARG 0.004 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 190 time to evaluate : 0.927 Fit side-chains REVERT: A 76 LYS cc_start: 0.7145 (ptmt) cc_final: 0.6694 (ptmm) REVERT: A 78 GLN cc_start: 0.7228 (tm-30) cc_final: 0.6986 (tm-30) REVERT: A 101 LEU cc_start: 0.8749 (mt) cc_final: 0.8522 (tt) REVERT: A 120 LYS cc_start: 0.8599 (tppt) cc_final: 0.7787 (tmmt) REVERT: A 165 ARG cc_start: 0.7344 (ttp80) cc_final: 0.7061 (ttt-90) REVERT: A 206 LEU cc_start: 0.8381 (mp) cc_final: 0.7806 (mp) REVERT: A 320 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8809 (t) REVERT: B 76 LYS cc_start: 0.7146 (ptmt) cc_final: 0.6695 (ptmm) REVERT: B 78 GLN cc_start: 0.7276 (tm-30) cc_final: 0.7033 (tm-30) REVERT: B 101 LEU cc_start: 0.8790 (mt) cc_final: 0.8554 (tt) REVERT: B 120 LYS cc_start: 0.8589 (tppt) cc_final: 0.7800 (tmmt) REVERT: B 127 TYR cc_start: 0.6777 (t80) cc_final: 0.6204 (m-80) REVERT: B 165 ARG cc_start: 0.7346 (ttp80) cc_final: 0.7077 (ttt-90) REVERT: B 206 LEU cc_start: 0.8393 (mp) cc_final: 0.7824 (mp) REVERT: B 320 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8826 (t) REVERT: C 76 LYS cc_start: 0.7119 (ptmt) cc_final: 0.6658 (ptmm) REVERT: C 78 GLN cc_start: 0.7236 (tm-30) cc_final: 0.6994 (tm-30) REVERT: C 101 LEU cc_start: 0.8733 (mt) cc_final: 0.8496 (tt) REVERT: C 120 LYS cc_start: 0.8583 (tppt) cc_final: 0.7792 (tmmt) REVERT: C 127 TYR cc_start: 0.6703 (t80) cc_final: 0.6151 (m-80) REVERT: C 165 ARG cc_start: 0.7346 (ttp80) cc_final: 0.7074 (ttt-90) REVERT: C 206 LEU cc_start: 0.8358 (mp) cc_final: 0.7800 (mp) REVERT: D 76 LYS cc_start: 0.7120 (ptmt) cc_final: 0.6665 (ptmm) REVERT: D 78 GLN cc_start: 0.7319 (tm-30) cc_final: 0.7047 (tm-30) REVERT: D 101 LEU cc_start: 0.8751 (mt) cc_final: 0.8518 (tt) REVERT: D 120 LYS cc_start: 0.8610 (tppt) cc_final: 0.7781 (tmmt) REVERT: D 127 TYR cc_start: 0.6766 (t80) cc_final: 0.6108 (m-80) REVERT: D 165 ARG cc_start: 0.7306 (ttp80) cc_final: 0.7016 (ttt-90) REVERT: D 206 LEU cc_start: 0.8399 (mp) cc_final: 0.7829 (mp) REVERT: D 320 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8826 (t) outliers start: 29 outliers final: 15 residues processed: 206 average time/residue: 0.2317 time to fit residues: 62.4008 Evaluate side-chains 195 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 118 TYR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.0050 chunk 61 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8448 Z= 0.175 Angle : 0.505 6.066 11436 Z= 0.260 Chirality : 0.035 0.136 1248 Planarity : 0.003 0.030 1384 Dihedral : 3.705 12.288 1124 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.71 % Allowed : 18.30 % Favored : 77.99 % 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 (0.27), residues: 984 helix: 2.26 (0.17), residues: 812 sheet: None (None), residues: 0 loop : -2.69 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 146 HIS 0.002 0.001 HIS C 328 PHE 0.014 0.001 PHE A 168 TYR 0.010 0.001 TYR A 74 ARG 0.004 0.000 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 179 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7194 (ptmt) cc_final: 0.6749 (ptmm) REVERT: A 78 GLN cc_start: 0.7235 (tm-30) cc_final: 0.6922 (tm-30) REVERT: A 101 LEU cc_start: 0.8712 (mt) cc_final: 0.8380 (tt) REVERT: A 120 LYS cc_start: 0.8633 (tppt) cc_final: 0.7835 (tmmt) REVERT: A 127 TYR cc_start: 0.6774 (t80) cc_final: 0.6140 (m-80) REVERT: A 165 ARG cc_start: 0.7409 (ttp80) cc_final: 0.7136 (ttt-90) REVERT: A 206 LEU cc_start: 0.8376 (mp) cc_final: 0.7814 (mp) REVERT: B 76 LYS cc_start: 0.7189 (ptmt) cc_final: 0.6735 (ptmm) REVERT: B 78 GLN cc_start: 0.7223 (tm-30) cc_final: 0.6891 (tm-30) REVERT: B 101 LEU cc_start: 0.8700 (mt) cc_final: 0.8333 (tt) REVERT: B 120 LYS cc_start: 0.8604 (tppt) cc_final: 0.7802 (tmmt) REVERT: B 127 TYR cc_start: 0.6783 (t80) cc_final: 0.6126 (m-80) REVERT: B 158 ARG cc_start: 0.6551 (tpt170) cc_final: 0.6329 (mtp85) REVERT: B 165 ARG cc_start: 0.7368 (ttp80) cc_final: 0.7105 (ttt-90) REVERT: B 206 LEU cc_start: 0.8353 (mp) cc_final: 0.7790 (mp) REVERT: B 320 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8770 (t) REVERT: C 76 LYS cc_start: 0.7170 (ptmt) cc_final: 0.6719 (ptmm) REVERT: C 78 GLN cc_start: 0.7205 (tm-30) cc_final: 0.6884 (tm-30) REVERT: C 101 LEU cc_start: 0.8700 (mt) cc_final: 0.8378 (tt) REVERT: C 120 LYS cc_start: 0.8622 (tppt) cc_final: 0.7823 (tmmt) REVERT: C 127 TYR cc_start: 0.6697 (t80) cc_final: 0.6089 (m-80) REVERT: C 158 ARG cc_start: 0.6517 (tpt170) cc_final: 0.6298 (mtp85) REVERT: C 165 ARG cc_start: 0.7291 (ttp80) cc_final: 0.7011 (ttt-90) REVERT: C 206 LEU cc_start: 0.8362 (mp) cc_final: 0.7808 (mp) REVERT: D 76 LYS cc_start: 0.7190 (ptmt) cc_final: 0.6740 (ptmm) REVERT: D 78 GLN cc_start: 0.7244 (tm-30) cc_final: 0.6914 (tm-30) REVERT: D 101 LEU cc_start: 0.8683 (mt) cc_final: 0.8373 (tt) REVERT: D 120 LYS cc_start: 0.8607 (tppt) cc_final: 0.7794 (tmmt) REVERT: D 127 TYR cc_start: 0.6757 (t80) cc_final: 0.6128 (m-80) REVERT: D 165 ARG cc_start: 0.7334 (ttp80) cc_final: 0.7060 (ttt-90) REVERT: D 206 LEU cc_start: 0.8329 (mp) cc_final: 0.7785 (mp) outliers start: 31 outliers final: 12 residues processed: 197 average time/residue: 0.2421 time to fit residues: 61.9789 Evaluate side-chains 182 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 231 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 323 GLN B 204 GLN C 204 GLN D 204 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8448 Z= 0.216 Angle : 0.500 5.495 11436 Z= 0.260 Chirality : 0.036 0.127 1248 Planarity : 0.003 0.028 1384 Dihedral : 3.667 11.874 1124 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.99 % Allowed : 18.66 % Favored : 78.35 % 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: 2.44 (0.27), residues: 984 helix: 2.41 (0.17), residues: 812 sheet: None (None), residues: 0 loop : -2.51 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.002 0.001 HIS D 328 PHE 0.016 0.001 PHE D 168 TYR 0.009 0.001 TYR D 284 ARG 0.004 0.000 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 0.918 Fit side-chains REVERT: A 76 LYS cc_start: 0.7245 (ptmt) cc_final: 0.6796 (ptmm) REVERT: A 78 GLN cc_start: 0.7215 (tm-30) cc_final: 0.6907 (tm-30) REVERT: A 101 LEU cc_start: 0.8655 (mt) cc_final: 0.8369 (tt) REVERT: A 120 LYS cc_start: 0.8638 (tppt) cc_final: 0.7824 (tmmt) REVERT: A 127 TYR cc_start: 0.6732 (t80) cc_final: 0.6134 (m-80) REVERT: A 206 LEU cc_start: 0.8383 (mp) cc_final: 0.7833 (mp) REVERT: B 76 LYS cc_start: 0.7211 (ptmt) cc_final: 0.6890 (pttt) REVERT: B 78 GLN cc_start: 0.7248 (tm-30) cc_final: 0.6971 (tm-30) REVERT: B 86 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6405 (mm-30) REVERT: B 101 LEU cc_start: 0.8685 (mt) cc_final: 0.8348 (tt) REVERT: B 120 LYS cc_start: 0.8607 (tppt) cc_final: 0.7822 (tmmt) REVERT: B 127 TYR cc_start: 0.6760 (t80) cc_final: 0.6112 (m-80) REVERT: B 158 ARG cc_start: 0.6573 (tpt170) cc_final: 0.6351 (mtp85) REVERT: B 206 LEU cc_start: 0.8376 (mp) cc_final: 0.7840 (mp) REVERT: C 76 LYS cc_start: 0.7220 (ptmt) cc_final: 0.6767 (ptmm) REVERT: C 78 GLN cc_start: 0.7209 (tm-30) cc_final: 0.6906 (tm-30) REVERT: C 120 LYS cc_start: 0.8616 (tppt) cc_final: 0.7821 (tmmt) REVERT: C 127 TYR cc_start: 0.6660 (t80) cc_final: 0.6076 (m-80) REVERT: C 158 ARG cc_start: 0.6558 (tpt170) cc_final: 0.6330 (mtp85) REVERT: C 165 ARG cc_start: 0.7429 (ttp80) cc_final: 0.7158 (ttt-90) REVERT: C 206 LEU cc_start: 0.8360 (mp) cc_final: 0.7825 (mp) REVERT: D 76 LYS cc_start: 0.7243 (ptmt) cc_final: 0.6928 (pttt) REVERT: D 78 GLN cc_start: 0.7209 (tm-30) cc_final: 0.6954 (tm-30) REVERT: D 101 LEU cc_start: 0.8648 (mt) cc_final: 0.8363 (tt) REVERT: D 120 LYS cc_start: 0.8604 (tppt) cc_final: 0.7784 (tmmt) REVERT: D 127 TYR cc_start: 0.6795 (t80) cc_final: 0.6126 (m-80) REVERT: D 165 ARG cc_start: 0.7385 (ttp80) cc_final: 0.7101 (ttp80) REVERT: D 206 LEU cc_start: 0.8366 (mp) cc_final: 0.7828 (mp) REVERT: D 213 ARG cc_start: 0.6931 (ttt180) cc_final: 0.6614 (ttp-170) outliers start: 25 outliers final: 17 residues processed: 187 average time/residue: 0.2277 time to fit residues: 56.1027 Evaluate side-chains 183 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN D 96 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8448 Z= 0.211 Angle : 0.494 7.798 11436 Z= 0.254 Chirality : 0.035 0.135 1248 Planarity : 0.003 0.029 1384 Dihedral : 3.627 13.312 1124 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.39 % Allowed : 19.74 % Favored : 77.87 % 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: 2.64 (0.27), residues: 984 helix: 2.51 (0.17), residues: 812 sheet: None (None), residues: 0 loop : -2.23 (0.50), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.002 0.001 HIS B 328 PHE 0.012 0.001 PHE D 168 TYR 0.009 0.001 TYR D 284 ARG 0.005 0.000 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 171 time to evaluate : 0.924 Fit side-chains REVERT: A 76 LYS cc_start: 0.7283 (ptmt) cc_final: 0.6835 (ptmm) REVERT: A 78 GLN cc_start: 0.7133 (tm-30) cc_final: 0.6858 (tm-30) REVERT: A 86 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7062 (mm-30) REVERT: A 120 LYS cc_start: 0.8635 (tppt) cc_final: 0.7816 (tmmt) REVERT: A 127 TYR cc_start: 0.6894 (t80) cc_final: 0.6206 (m-80) REVERT: A 158 ARG cc_start: 0.6505 (tpt170) cc_final: 0.6208 (mtp85) REVERT: A 206 LEU cc_start: 0.8360 (mp) cc_final: 0.7833 (mp) REVERT: B 76 LYS cc_start: 0.7322 (ptmt) cc_final: 0.7002 (pttt) REVERT: B 78 GLN cc_start: 0.7131 (tm-30) cc_final: 0.6867 (tm-30) REVERT: B 101 LEU cc_start: 0.8702 (mt) cc_final: 0.8377 (tt) REVERT: B 120 LYS cc_start: 0.8605 (tppt) cc_final: 0.7821 (tmmt) REVERT: B 127 TYR cc_start: 0.6875 (t80) cc_final: 0.6190 (m-80) REVERT: B 158 ARG cc_start: 0.6595 (tpt170) cc_final: 0.6391 (mtp85) REVERT: B 206 LEU cc_start: 0.8367 (mp) cc_final: 0.7817 (mp) REVERT: B 213 ARG cc_start: 0.7028 (ttt180) cc_final: 0.6818 (ttt180) REVERT: C 76 LYS cc_start: 0.7237 (ptmt) cc_final: 0.6900 (pttt) REVERT: C 78 GLN cc_start: 0.7186 (tm-30) cc_final: 0.6930 (tm-30) REVERT: C 120 LYS cc_start: 0.8625 (tppt) cc_final: 0.7848 (tmmt) REVERT: C 127 TYR cc_start: 0.6700 (t80) cc_final: 0.6103 (m-80) REVERT: C 206 LEU cc_start: 0.8356 (mp) cc_final: 0.7836 (mp) REVERT: D 76 LYS cc_start: 0.7266 (ptmt) cc_final: 0.6942 (pttt) REVERT: D 78 GLN cc_start: 0.7133 (tm-30) cc_final: 0.6865 (tm-30) REVERT: D 86 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6820 (mm-30) REVERT: D 120 LYS cc_start: 0.8602 (tppt) cc_final: 0.7783 (tmmt) REVERT: D 127 TYR cc_start: 0.6813 (t80) cc_final: 0.6171 (m-80) REVERT: D 206 LEU cc_start: 0.8352 (mp) cc_final: 0.7828 (mp) outliers start: 20 outliers final: 11 residues processed: 181 average time/residue: 0.2301 time to fit residues: 54.5921 Evaluate side-chains 173 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 162 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 241 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 8.9990 chunk 70 optimal weight: 0.0270 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN C 204 GLN D 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8448 Z= 0.191 Angle : 0.488 7.329 11436 Z= 0.250 Chirality : 0.034 0.120 1248 Planarity : 0.003 0.030 1384 Dihedral : 3.580 14.272 1124 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.11 % Allowed : 18.78 % Favored : 78.11 % 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: 2.81 (0.27), residues: 984 helix: 2.60 (0.17), residues: 812 sheet: None (None), residues: 0 loop : -2.03 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 146 HIS 0.002 0.001 HIS B 328 PHE 0.016 0.001 PHE A 168 TYR 0.009 0.001 TYR D 284 ARG 0.007 0.000 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7339 (ptmt) cc_final: 0.7032 (pttt) REVERT: A 78 GLN cc_start: 0.7135 (tm-30) cc_final: 0.6872 (tm-30) REVERT: A 86 GLU cc_start: 0.6987 (mm-30) cc_final: 0.5936 (mm-30) REVERT: A 120 LYS cc_start: 0.8637 (tppt) cc_final: 0.7806 (tmmt) REVERT: A 127 TYR cc_start: 0.6763 (t80) cc_final: 0.6152 (m-80) REVERT: A 158 ARG cc_start: 0.6471 (tpt170) cc_final: 0.6170 (mtp85) REVERT: A 206 LEU cc_start: 0.8322 (mp) cc_final: 0.7819 (mp) REVERT: B 76 LYS cc_start: 0.7376 (ptmt) cc_final: 0.7053 (pttt) REVERT: B 78 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6835 (tm-30) REVERT: B 120 LYS cc_start: 0.8583 (tppt) cc_final: 0.7787 (tmmt) REVERT: B 127 TYR cc_start: 0.6964 (t80) cc_final: 0.6198 (m-80) REVERT: B 206 LEU cc_start: 0.8351 (mp) cc_final: 0.7860 (mp) REVERT: C 76 LYS cc_start: 0.7320 (ptmt) cc_final: 0.6985 (pttt) REVERT: C 78 GLN cc_start: 0.7043 (tm-30) cc_final: 0.6795 (tm-30) REVERT: C 86 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6966 (mm-30) REVERT: C 120 LYS cc_start: 0.8588 (tppt) cc_final: 0.7785 (tmmt) REVERT: C 127 TYR cc_start: 0.6864 (t80) cc_final: 0.6160 (m-80) REVERT: C 206 LEU cc_start: 0.8321 (mp) cc_final: 0.7845 (mp) REVERT: D 76 LYS cc_start: 0.7322 (ptmt) cc_final: 0.6994 (pttt) REVERT: D 78 GLN cc_start: 0.7064 (tm-30) cc_final: 0.6812 (tm-30) REVERT: D 120 LYS cc_start: 0.8575 (tppt) cc_final: 0.7765 (tmmt) REVERT: D 127 TYR cc_start: 0.6841 (t80) cc_final: 0.6183 (m-80) REVERT: D 206 LEU cc_start: 0.8327 (mp) cc_final: 0.7823 (mp) outliers start: 26 outliers final: 17 residues processed: 185 average time/residue: 0.1985 time to fit residues: 49.9588 Evaluate side-chains 177 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8448 Z= 0.244 Angle : 0.528 7.245 11436 Z= 0.268 Chirality : 0.037 0.306 1248 Planarity : 0.003 0.049 1384 Dihedral : 3.592 13.037 1124 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.87 % Allowed : 18.90 % Favored : 78.23 % 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: 2.80 (0.27), residues: 984 helix: 2.56 (0.17), residues: 812 sheet: None (None), residues: 0 loop : -1.85 (0.54), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 146 HIS 0.002 0.001 HIS A 328 PHE 0.010 0.001 PHE C 168 TYR 0.010 0.001 TYR D 284 ARG 0.009 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7335 (ptmt) cc_final: 0.7015 (pttt) REVERT: A 78 GLN cc_start: 0.7123 (tm-30) cc_final: 0.6850 (tm-30) REVERT: A 86 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6492 (mm-30) REVERT: A 120 LYS cc_start: 0.8639 (tppt) cc_final: 0.7806 (tmmt) REVERT: A 127 TYR cc_start: 0.6866 (t80) cc_final: 0.6223 (m-80) REVERT: A 158 ARG cc_start: 0.6488 (tpt170) cc_final: 0.6202 (mtp85) REVERT: A 206 LEU cc_start: 0.8352 (mp) cc_final: 0.7850 (mp) REVERT: B 76 LYS cc_start: 0.7334 (ptmt) cc_final: 0.7031 (pttt) REVERT: B 78 GLN cc_start: 0.7123 (tm-30) cc_final: 0.6885 (tm-30) REVERT: B 93 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6839 (t80) REVERT: B 120 LYS cc_start: 0.8559 (tppt) cc_final: 0.7795 (tmmt) REVERT: B 127 TYR cc_start: 0.7011 (t80) cc_final: 0.6249 (m-80) REVERT: B 206 LEU cc_start: 0.8358 (mp) cc_final: 0.7858 (mp) REVERT: C 76 LYS cc_start: 0.7333 (ptmt) cc_final: 0.6992 (pttt) REVERT: C 78 GLN cc_start: 0.7082 (tm-30) cc_final: 0.6871 (tm-30) REVERT: C 120 LYS cc_start: 0.8590 (tppt) cc_final: 0.7834 (tmmt) REVERT: C 127 TYR cc_start: 0.6991 (t80) cc_final: 0.6244 (m-80) REVERT: C 206 LEU cc_start: 0.8350 (mp) cc_final: 0.7858 (mp) REVERT: D 76 LYS cc_start: 0.7340 (ptmt) cc_final: 0.7032 (pttt) REVERT: D 78 GLN cc_start: 0.7101 (tm-30) cc_final: 0.6836 (tm-30) REVERT: D 93 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6852 (t80) REVERT: D 120 LYS cc_start: 0.8582 (tppt) cc_final: 0.7787 (tmmt) REVERT: D 127 TYR cc_start: 0.6813 (t80) cc_final: 0.6212 (m-80) REVERT: D 206 LEU cc_start: 0.8348 (mp) cc_final: 0.7830 (mp) outliers start: 24 outliers final: 19 residues processed: 182 average time/residue: 0.1943 time to fit residues: 48.0808 Evaluate side-chains 175 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 0.0040 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.0870 chunk 58 optimal weight: 20.0000 chunk 94 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 overall best weight: 0.4570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8448 Z= 0.165 Angle : 0.517 10.065 11436 Z= 0.257 Chirality : 0.038 0.333 1248 Planarity : 0.003 0.029 1384 Dihedral : 3.514 14.946 1124 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.15 % Allowed : 19.86 % Favored : 77.99 % 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: 2.81 (0.27), residues: 984 helix: 2.55 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -1.65 (0.53), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.002 0.000 HIS B 328 PHE 0.015 0.001 PHE B 168 TYR 0.011 0.001 TYR B 74 ARG 0.006 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7475 (ptmt) cc_final: 0.7142 (pttt) REVERT: A 78 GLN cc_start: 0.7096 (tm-30) cc_final: 0.6860 (tm-30) REVERT: A 120 LYS cc_start: 0.8615 (tppt) cc_final: 0.7774 (tmmt) REVERT: A 127 TYR cc_start: 0.6826 (t80) cc_final: 0.6196 (m-80) REVERT: A 158 ARG cc_start: 0.6516 (tpt170) cc_final: 0.6245 (mtp85) REVERT: A 206 LEU cc_start: 0.8292 (mp) cc_final: 0.7839 (mp) REVERT: B 76 LYS cc_start: 0.7422 (ptmt) cc_final: 0.7095 (pttt) REVERT: B 78 GLN cc_start: 0.7095 (tm-30) cc_final: 0.6840 (tm-30) REVERT: B 120 LYS cc_start: 0.8552 (tppt) cc_final: 0.7778 (tmmt) REVERT: B 127 TYR cc_start: 0.6882 (t80) cc_final: 0.6166 (m-80) REVERT: B 206 LEU cc_start: 0.8297 (mp) cc_final: 0.7853 (mp) REVERT: C 76 LYS cc_start: 0.7388 (ptmt) cc_final: 0.7047 (pttt) REVERT: C 78 GLN cc_start: 0.7093 (tm-30) cc_final: 0.6849 (tm-30) REVERT: C 120 LYS cc_start: 0.8540 (tppt) cc_final: 0.7759 (tmmt) REVERT: C 127 TYR cc_start: 0.7043 (t80) cc_final: 0.6251 (m-80) REVERT: C 206 LEU cc_start: 0.8294 (mp) cc_final: 0.7850 (mp) REVERT: D 76 LYS cc_start: 0.7411 (ptmt) cc_final: 0.7078 (pttt) REVERT: D 78 GLN cc_start: 0.7115 (tm-30) cc_final: 0.6855 (tm-30) REVERT: D 120 LYS cc_start: 0.8565 (tppt) cc_final: 0.7760 (tmmt) REVERT: D 127 TYR cc_start: 0.6828 (t80) cc_final: 0.6182 (m-80) REVERT: D 206 LEU cc_start: 0.8305 (mp) cc_final: 0.7843 (mp) outliers start: 18 outliers final: 18 residues processed: 172 average time/residue: 0.2102 time to fit residues: 49.1671 Evaluate side-chains 173 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 204 GLN C 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8448 Z= 0.231 Angle : 0.549 9.753 11436 Z= 0.276 Chirality : 0.040 0.349 1248 Planarity : 0.003 0.031 1384 Dihedral : 3.529 13.224 1124 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.63 % Allowed : 19.38 % Favored : 77.99 % 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: 2.79 (0.27), residues: 984 helix: 2.55 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -1.72 (0.52), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 146 HIS 0.002 0.001 HIS A 328 PHE 0.017 0.001 PHE B 168 TYR 0.010 0.001 TYR D 284 ARG 0.005 0.000 ARG B 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 0.930 Fit side-chains REVERT: A 76 LYS cc_start: 0.7441 (ptmt) cc_final: 0.7130 (pttt) REVERT: A 78 GLN cc_start: 0.7140 (tm-30) cc_final: 0.6893 (tm-30) REVERT: A 120 LYS cc_start: 0.8616 (tppt) cc_final: 0.7802 (tmmt) REVERT: A 127 TYR cc_start: 0.6888 (t80) cc_final: 0.6244 (m-80) REVERT: A 158 ARG cc_start: 0.6535 (tpt170) cc_final: 0.6275 (mtp85) REVERT: A 206 LEU cc_start: 0.8319 (mp) cc_final: 0.7840 (mp) REVERT: B 76 LYS cc_start: 0.7316 (ptmt) cc_final: 0.7007 (pttt) REVERT: B 78 GLN cc_start: 0.7164 (tm-30) cc_final: 0.6910 (tm-30) REVERT: B 120 LYS cc_start: 0.8554 (tppt) cc_final: 0.7783 (tmmt) REVERT: B 127 TYR cc_start: 0.6966 (t80) cc_final: 0.6228 (m-80) REVERT: B 206 LEU cc_start: 0.8335 (mp) cc_final: 0.7863 (mp) REVERT: C 76 LYS cc_start: 0.7394 (ptmt) cc_final: 0.7077 (pttt) REVERT: C 78 GLN cc_start: 0.7141 (tm-30) cc_final: 0.6892 (tm-30) REVERT: C 120 LYS cc_start: 0.8575 (tppt) cc_final: 0.7806 (tmmt) REVERT: C 127 TYR cc_start: 0.7107 (t80) cc_final: 0.6294 (m-80) REVERT: C 206 LEU cc_start: 0.8328 (mp) cc_final: 0.7853 (mp) REVERT: D 76 LYS cc_start: 0.7404 (ptmt) cc_final: 0.7086 (pttt) REVERT: D 78 GLN cc_start: 0.7136 (tm-30) cc_final: 0.6868 (tm-30) REVERT: D 93 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6765 (t80) REVERT: D 120 LYS cc_start: 0.8570 (tppt) cc_final: 0.7767 (tmmt) REVERT: D 127 TYR cc_start: 0.6755 (t80) cc_final: 0.6135 (m-80) REVERT: D 206 LEU cc_start: 0.8331 (mp) cc_final: 0.7850 (mp) outliers start: 22 outliers final: 20 residues processed: 175 average time/residue: 0.1997 time to fit residues: 47.5309 Evaluate side-chains 175 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 TYR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.0270 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.208049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.164399 restraints weight = 9402.997| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.12 r_work: 0.3371 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8448 Z= 0.215 Angle : 0.550 11.744 11436 Z= 0.275 Chirality : 0.041 0.342 1248 Planarity : 0.003 0.050 1384 Dihedral : 3.518 13.010 1124 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.99 % Allowed : 19.02 % Favored : 77.99 % 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: 2.75 (0.27), residues: 984 helix: 2.51 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -1.67 (0.52), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 146 HIS 0.002 0.001 HIS D 328 PHE 0.016 0.001 PHE B 168 TYR 0.010 0.001 TYR D 284 ARG 0.004 0.000 ARG B 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1976.00 seconds wall clock time: 35 minutes 44.76 seconds (2144.76 seconds total)