Starting phenix.real_space_refine on Fri Jul 19 09:56:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk3_18455/07_2024/8qk3_18455.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk3_18455/07_2024/8qk3_18455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk3_18455/07_2024/8qk3_18455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk3_18455/07_2024/8qk3_18455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk3_18455/07_2024/8qk3_18455.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk3_18455/07_2024/8qk3_18455.cif" } resolution = 3.2 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= 0.002 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4754 2.51 5 N 1241 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D GLU 240": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7535 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "C" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1548 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "E" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1018 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 113} Chain: "D" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1873 Classifications: {'peptide': 238} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 227} Time building chain proxies: 4.96, per 1000 atoms: 0.66 Number of scatterers: 7535 At special positions: 0 Unit cell: (106.68, 122.64, 96.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1500 8.00 N 1241 7.00 C 4754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 1 " - pdb=" SG CYS E 46 " distance=2.03 Simple disulfide: pdb=" SG CYS E 30 " - pdb=" SG CYS E 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 107 " distance=1.38 Simple disulfide: pdb=" SG CYS E 93 " - pdb=" SG CYS E 123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.74 Conformation dependent library (CDL) restraints added in 2.2 seconds 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1814 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 18 sheets defined 6.8% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 249 through 252 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 246 through 252 removed outlier: 5.413A pdb=" N LYS A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 249 through 252 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing sheet with id=AA1, first strand: chain 'B' and resid 133 through 135 Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 199 removed outlier: 5.674A pdb=" N ASN B 297 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 135 Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 199 removed outlier: 6.272A pdb=" N ASN A 297 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA7, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AA8, first strand: chain 'C' and resid 190 through 199 removed outlier: 6.419A pdb=" N ASN C 297 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 219 through 220 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 34 through 36 Processing sheet with id=AB3, first strand: chain 'E' and resid 74 through 78 removed outlier: 3.831A pdb=" N TYR E 87 " --> pdb=" O CYS E 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 97 through 99 Processing sheet with id=AB5, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AB6, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.739A pdb=" N PHE D 115 " --> pdb=" O GLN D 210 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ARG D 212 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY D 117 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU D 214 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL D 119 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR D 187 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU D 154 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR D 189 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.635A pdb=" N ILE D 171 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 222 through 223 removed outlier: 6.766A pdb=" N VAL D 285 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG D 243 " --> pdb=" O GLY D 283 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY D 283 " --> pdb=" O ARG D 243 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 229 through 232 removed outlier: 6.626A pdb=" N SER D 302 " --> pdb=" O ALA D 264 " (cutoff:3.500A) 212 hydrogen bonds defined for protein. 528 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: 1.95 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1355 1.32 - 1.45: 2045 1.45 - 1.57: 4240 1.57 - 1.69: 0 1.69 - 1.82: 60 Bond restraints: 7700 Sorted by residual: bond pdb=" C PRO E 4 " pdb=" O PRO E 4 " ideal model delta sigma weight residual 1.240 1.207 0.033 1.12e-02 7.97e+03 8.67e+00 bond pdb=" N TYR E 20 " pdb=" CA TYR E 20 " ideal model delta sigma weight residual 1.457 1.490 -0.034 1.24e-02 6.50e+03 7.32e+00 bond pdb=" C PRO E 5 " pdb=" O PRO E 5 " ideal model delta sigma weight residual 1.233 1.202 0.031 1.19e-02 7.06e+03 6.86e+00 bond pdb=" N TRP E 52 " pdb=" CA TRP E 52 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.22e-02 6.72e+03 4.85e+00 bond pdb=" C TYR B 242 " pdb=" N PRO B 243 " ideal model delta sigma weight residual 1.328 1.353 -0.025 1.25e-02 6.40e+03 4.09e+00 ... (remaining 7695 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.13: 248 107.13 - 113.90: 4297 113.90 - 120.67: 2933 120.67 - 127.45: 2944 127.45 - 134.22: 75 Bond angle restraints: 10497 Sorted by residual: angle pdb=" N PRO E 4 " pdb=" CA PRO E 4 " pdb=" C PRO E 4 " ideal model delta sigma weight residual 110.70 105.76 4.94 1.22e+00 6.72e-01 1.64e+01 angle pdb=" N GLU E 2 " pdb=" CA GLU E 2 " pdb=" C GLU E 2 " ideal model delta sigma weight residual 113.89 108.62 5.27 1.58e+00 4.01e-01 1.11e+01 angle pdb=" C GLU E 2 " pdb=" N GLU E 3 " pdb=" CA GLU E 3 " ideal model delta sigma weight residual 122.26 118.69 3.57 1.10e+00 8.26e-01 1.06e+01 angle pdb=" N VAL D 129 " pdb=" CA VAL D 129 " pdb=" C VAL D 129 " ideal model delta sigma weight residual 111.45 108.49 2.96 9.30e-01 1.16e+00 1.01e+01 angle pdb=" N ASN A 278 " pdb=" CA ASN A 278 " pdb=" C ASN A 278 " ideal model delta sigma weight residual 111.30 115.56 -4.26 1.36e+00 5.41e-01 9.83e+00 ... (remaining 10492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4287 17.61 - 35.22: 241 35.22 - 52.83: 52 52.83 - 70.44: 16 70.44 - 88.05: 5 Dihedral angle restraints: 4601 sinusoidal: 1790 harmonic: 2811 Sorted by residual: dihedral pdb=" CA SER A 153 " pdb=" C SER A 153 " pdb=" N ASN A 154 " pdb=" CA ASN A 154 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASN B 154 " pdb=" C ASN B 154 " pdb=" N ASP B 155 " pdb=" CA ASP B 155 " ideal model delta harmonic sigma weight residual 180.00 -156.27 -23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA SER B 153 " pdb=" C SER B 153 " pdb=" N ASN B 154 " pdb=" CA ASN B 154 " ideal model delta harmonic sigma weight residual 180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 4598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 734 0.031 - 0.062: 315 0.062 - 0.093: 58 0.093 - 0.124: 74 0.124 - 0.155: 20 Chirality restraints: 1201 Sorted by residual: chirality pdb=" CA PRO E 4 " pdb=" N PRO E 4 " pdb=" C PRO E 4 " pdb=" CB PRO E 4 " both_signs ideal model delta sigma weight residual False 2.72 2.87 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ILE D 324 " pdb=" N ILE D 324 " pdb=" C ILE D 324 " pdb=" CB ILE D 324 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA ASN A 278 " pdb=" N ASN A 278 " pdb=" C ASN A 278 " pdb=" CB ASN A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 1198 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 158 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.14e+00 pdb=" N PRO D 159 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 159 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 159 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 53 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO E 54 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 54 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 54 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 324 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO D 325 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 325 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 325 " 0.027 5.00e-02 4.00e+02 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 58 2.51 - 3.11: 5735 3.11 - 3.71: 11235 3.71 - 4.30: 16926 4.30 - 4.90: 28155 Nonbonded interactions: 62109 Sorted by model distance: nonbonded pdb=" OE1 GLU D 170 " pdb=" OH TYR D 172 " model vdw 1.913 2.440 nonbonded pdb=" O GLU D 120 " pdb=" OG SER D 123 " model vdw 1.931 2.440 nonbonded pdb=" OG1 THR D 280 " pdb=" OE2 GLU D 282 " model vdw 2.075 2.440 nonbonded pdb=" OG SER A 264 " pdb=" OE2 GLU A 303 " model vdw 2.115 2.440 nonbonded pdb=" NZ LYS A 233 " pdb=" OH TYR A 288 " model vdw 2.136 2.520 ... (remaining 62104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.710 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 0.044 7700 Z= 0.208 Angle : 0.597 6.412 10497 Z= 0.356 Chirality : 0.045 0.155 1201 Planarity : 0.004 0.051 1360 Dihedral : 12.490 88.050 2775 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.12 % Allowed : 12.50 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.49 (0.27), residues: 945 helix: -0.25 (1.26), residues: 21 sheet: -0.33 (0.26), residues: 354 loop : -0.22 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 296 HIS 0.004 0.001 HIS A 218 PHE 0.016 0.001 PHE C 172 TYR 0.012 0.001 TYR D 172 ARG 0.003 0.000 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 TYR cc_start: 0.8172 (m-80) cc_final: 0.7945 (m-80) REVERT: B 324 ASP cc_start: 0.7534 (m-30) cc_final: 0.7331 (m-30) REVERT: A 182 PHE cc_start: 0.8180 (t80) cc_final: 0.7947 (t80) REVERT: A 184 MET cc_start: 0.8364 (ppp) cc_final: 0.8090 (ppp) REVERT: A 319 TYR cc_start: 0.8224 (m-80) cc_final: 0.7949 (m-80) REVERT: C 280 ARG cc_start: 0.8287 (mtt-85) cc_final: 0.7837 (mtt-85) REVERT: E 99 LEU cc_start: 0.8643 (tp) cc_final: 0.7805 (mt) REVERT: D 231 MET cc_start: 0.7852 (tpp) cc_final: 0.7530 (tpt) REVERT: D 301 PHE cc_start: 0.7552 (p90) cc_final: 0.7310 (p90) outliers start: 1 outliers final: 1 residues processed: 238 average time/residue: 0.2626 time to fit residues: 77.6772 Evaluate side-chains 157 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 0.0870 chunk 43 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN E 90 HIS ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7700 Z= 0.290 Angle : 0.633 10.138 10497 Z= 0.335 Chirality : 0.046 0.273 1201 Planarity : 0.004 0.034 1360 Dihedral : 4.866 26.921 1035 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.25 % Allowed : 15.57 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.59 (0.27), residues: 945 helix: -0.08 (1.27), residues: 21 sheet: -0.47 (0.26), residues: 347 loop : -0.26 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 52 HIS 0.003 0.001 HIS A 218 PHE 0.023 0.002 PHE E 85 TYR 0.026 0.002 TYR D 186 ARG 0.005 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 160 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 TYR cc_start: 0.7965 (m-80) cc_final: 0.7651 (m-80) REVERT: C 280 ARG cc_start: 0.8310 (mtt-85) cc_final: 0.7911 (mtt-85) REVERT: E 69 ARG cc_start: 0.8589 (mtm110) cc_final: 0.8347 (mtm110) REVERT: E 70 ASP cc_start: 0.8948 (m-30) cc_final: 0.8692 (t0) REVERT: E 99 LEU cc_start: 0.8157 (tp) cc_final: 0.7800 (mt) REVERT: E 116 TRP cc_start: 0.8331 (m100) cc_final: 0.8012 (m100) REVERT: D 186 TYR cc_start: 0.8304 (m-10) cc_final: 0.8099 (m-10) outliers start: 36 outliers final: 21 residues processed: 181 average time/residue: 0.2331 time to fit residues: 54.4416 Evaluate side-chains 163 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 142 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 ASN ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS E 50 HIS ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 7700 Z= 0.530 Angle : 0.705 10.047 10497 Z= 0.374 Chirality : 0.047 0.231 1201 Planarity : 0.004 0.035 1360 Dihedral : 5.374 36.498 1034 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.60 % Allowed : 16.04 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.78 (0.27), residues: 945 helix: -0.73 (0.90), residues: 36 sheet: -0.61 (0.26), residues: 351 loop : -0.33 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 296 HIS 0.012 0.002 HIS E 90 PHE 0.019 0.002 PHE E 91 TYR 0.022 0.002 TYR B 256 ARG 0.005 0.001 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 236 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8363 (mmm) REVERT: C 319 TYR cc_start: 0.7985 (m-80) cc_final: 0.7606 (m-80) REVERT: E 70 ASP cc_start: 0.8979 (m-30) cc_final: 0.8762 (t0) REVERT: E 99 LEU cc_start: 0.8306 (tp) cc_final: 0.7967 (tp) REVERT: E 116 TRP cc_start: 0.8384 (m100) cc_final: 0.7989 (m100) REVERT: D 112 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7772 (tm-30) REVERT: D 186 TYR cc_start: 0.8455 (m-80) cc_final: 0.8192 (m-10) REVERT: D 231 MET cc_start: 0.7851 (tpp) cc_final: 0.7210 (mpp) outliers start: 39 outliers final: 28 residues processed: 155 average time/residue: 0.2356 time to fit residues: 47.0622 Evaluate side-chains 152 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 123 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 30.0000 chunk 62 optimal weight: 0.0570 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 30.0000 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN C 231 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7700 Z= 0.205 Angle : 0.611 10.040 10497 Z= 0.319 Chirality : 0.045 0.212 1201 Planarity : 0.004 0.033 1360 Dihedral : 5.091 33.701 1034 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.77 % Allowed : 17.45 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.60 (0.27), residues: 945 helix: -0.65 (0.90), residues: 36 sheet: -0.57 (0.27), residues: 349 loop : -0.14 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 296 HIS 0.008 0.001 HIS E 90 PHE 0.024 0.002 PHE E 91 TYR 0.017 0.001 TYR E 106 ARG 0.006 0.001 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 70 ASP cc_start: 0.8967 (m-30) cc_final: 0.8724 (t0) REVERT: E 99 LEU cc_start: 0.8060 (tp) cc_final: 0.7599 (mt) REVERT: D 193 ARG cc_start: 0.6714 (mtm110) cc_final: 0.6216 (ptm160) outliers start: 32 outliers final: 23 residues processed: 158 average time/residue: 0.2380 time to fit residues: 48.4173 Evaluate side-chains 143 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7700 Z= 0.284 Angle : 0.639 9.551 10497 Z= 0.329 Chirality : 0.045 0.195 1201 Planarity : 0.004 0.034 1360 Dihedral : 5.073 33.110 1034 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.36 % Allowed : 17.22 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.54 (0.27), residues: 945 helix: -0.57 (0.92), residues: 36 sheet: -0.57 (0.27), residues: 336 loop : -0.10 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 116 HIS 0.008 0.001 HIS E 90 PHE 0.017 0.002 PHE D 110 TYR 0.023 0.001 TYR D 186 ARG 0.006 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 TYR cc_start: 0.7858 (m-80) cc_final: 0.7413 (m-80) REVERT: C 319 TYR cc_start: 0.7873 (m-80) cc_final: 0.7546 (m-80) REVERT: E 70 ASP cc_start: 0.8975 (m-30) cc_final: 0.8752 (t0) REVERT: E 99 LEU cc_start: 0.8074 (tp) cc_final: 0.7599 (mt) REVERT: D 193 ARG cc_start: 0.6737 (mtm110) cc_final: 0.6275 (ptm160) outliers start: 37 outliers final: 28 residues processed: 146 average time/residue: 0.2452 time to fit residues: 45.8926 Evaluate side-chains 145 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7700 Z= 0.282 Angle : 0.636 9.302 10497 Z= 0.329 Chirality : 0.045 0.175 1201 Planarity : 0.004 0.036 1360 Dihedral : 5.090 32.260 1034 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.66 % Allowed : 18.40 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.49 (0.27), residues: 945 helix: -0.68 (0.91), residues: 36 sheet: -0.49 (0.27), residues: 338 loop : -0.08 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 116 HIS 0.006 0.001 HIS E 90 PHE 0.024 0.002 PHE E 91 TYR 0.017 0.001 TYR B 256 ARG 0.010 0.001 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 124 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 TYR cc_start: 0.7838 (m-80) cc_final: 0.7408 (m-80) REVERT: A 319 TYR cc_start: 0.8024 (m-80) cc_final: 0.7762 (m-80) REVERT: C 319 TYR cc_start: 0.7882 (m-80) cc_final: 0.7483 (m-80) REVERT: E 99 LEU cc_start: 0.8035 (tp) cc_final: 0.7518 (mt) REVERT: D 193 ARG cc_start: 0.6825 (mtm110) cc_final: 0.6289 (ptm160) REVERT: D 231 MET cc_start: 0.7580 (tpp) cc_final: 0.6747 (mpp) outliers start: 31 outliers final: 30 residues processed: 143 average time/residue: 0.2434 time to fit residues: 44.7111 Evaluate side-chains 151 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7700 Z= 0.360 Angle : 0.668 8.795 10497 Z= 0.347 Chirality : 0.044 0.162 1201 Planarity : 0.004 0.038 1360 Dihedral : 5.137 32.227 1034 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.60 % Allowed : 17.81 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.51 (0.27), residues: 945 helix: -0.66 (0.92), residues: 36 sheet: -0.53 (0.27), residues: 339 loop : -0.07 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 296 HIS 0.006 0.001 HIS E 90 PHE 0.027 0.002 PHE E 91 TYR 0.016 0.001 TYR B 256 ARG 0.006 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 124 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7591 (mm-30) REVERT: B 319 TYR cc_start: 0.7862 (m-80) cc_final: 0.7433 (m-80) REVERT: A 319 TYR cc_start: 0.8010 (m-80) cc_final: 0.7744 (m-80) REVERT: C 319 TYR cc_start: 0.7932 (m-80) cc_final: 0.7478 (m-80) REVERT: E 99 LEU cc_start: 0.8011 (tp) cc_final: 0.7468 (mt) outliers start: 39 outliers final: 31 residues processed: 148 average time/residue: 0.2339 time to fit residues: 44.5385 Evaluate side-chains 147 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.0870 chunk 17 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN D 238 ASN D 279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7700 Z= 0.193 Angle : 0.641 8.906 10497 Z= 0.330 Chirality : 0.045 0.155 1201 Planarity : 0.004 0.035 1360 Dihedral : 4.940 30.888 1034 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.54 % Allowed : 19.81 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.41 (0.27), residues: 945 helix: -0.80 (0.88), residues: 36 sheet: -0.46 (0.27), residues: 339 loop : 0.01 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 296 HIS 0.005 0.001 HIS E 90 PHE 0.014 0.002 PHE C 172 TYR 0.014 0.001 TYR B 320 ARG 0.009 0.001 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 GLU cc_start: 0.8237 (pm20) cc_final: 0.8010 (pm20) REVERT: E 99 LEU cc_start: 0.7717 (tp) cc_final: 0.7089 (mt) REVERT: D 231 MET cc_start: 0.7588 (tpp) cc_final: 0.6665 (mpp) REVERT: D 279 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8054 (pp30) outliers start: 30 outliers final: 25 residues processed: 149 average time/residue: 0.2422 time to fit residues: 46.7647 Evaluate side-chains 145 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7700 Z= 0.242 Angle : 0.653 9.559 10497 Z= 0.336 Chirality : 0.044 0.148 1201 Planarity : 0.004 0.039 1360 Dihedral : 4.917 30.103 1034 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.30 % Allowed : 20.64 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.41 (0.27), residues: 945 helix: -0.69 (0.89), residues: 36 sheet: -0.46 (0.27), residues: 339 loop : 0.00 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 296 HIS 0.004 0.001 HIS E 90 PHE 0.013 0.002 PHE E 85 TYR 0.013 0.001 TYR A 319 ARG 0.007 0.001 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 GLU cc_start: 0.8264 (pm20) cc_final: 0.8025 (pm20) REVERT: C 319 TYR cc_start: 0.7815 (m-80) cc_final: 0.7581 (m-80) REVERT: D 231 MET cc_start: 0.7629 (tpp) cc_final: 0.6582 (mpp) outliers start: 28 outliers final: 27 residues processed: 132 average time/residue: 0.2333 time to fit residues: 39.8403 Evaluate side-chains 144 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 chunk 84 optimal weight: 0.0670 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7700 Z= 0.204 Angle : 0.658 10.046 10497 Z= 0.335 Chirality : 0.044 0.149 1201 Planarity : 0.004 0.044 1360 Dihedral : 4.765 33.248 1034 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.95 % Allowed : 20.99 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.31 (0.28), residues: 945 helix: -0.71 (0.90), residues: 36 sheet: -0.42 (0.28), residues: 335 loop : 0.10 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 296 HIS 0.003 0.001 HIS E 90 PHE 0.013 0.002 PHE E 85 TYR 0.013 0.001 TYR A 319 ARG 0.009 0.001 ARG D 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 250 GLU cc_start: 0.8244 (pm20) cc_final: 0.8012 (pm20) REVERT: D 231 MET cc_start: 0.7640 (tpp) cc_final: 0.6626 (mpp) outliers start: 25 outliers final: 23 residues processed: 144 average time/residue: 0.2253 time to fit residues: 41.8619 Evaluate side-chains 143 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 279 GLN Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 30 optimal weight: 0.0970 chunk 75 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.067897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.043523 restraints weight = 26619.678| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 4.42 r_work: 0.2634 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 7700 Z= 0.398 Angle : 0.701 9.948 10497 Z= 0.363 Chirality : 0.045 0.146 1201 Planarity : 0.004 0.048 1360 Dihedral : 5.025 31.156 1034 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.07 % Allowed : 21.46 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.45 (0.27), residues: 945 helix: -0.60 (0.91), residues: 36 sheet: -0.50 (0.27), residues: 335 loop : -0.03 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 296 HIS 0.004 0.001 HIS A 218 PHE 0.020 0.002 PHE E 91 TYR 0.013 0.002 TYR B 242 ARG 0.007 0.001 ARG D 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2132.15 seconds wall clock time: 39 minutes 13.62 seconds (2353.62 seconds total)