Starting phenix.real_space_refine on Thu Mar 6 09:01:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vae_31838/03_2025/7vae_31838.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vae_31838/03_2025/7vae_31838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vae_31838/03_2025/7vae_31838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vae_31838/03_2025/7vae_31838.map" model { file = "/net/cci-nas-00/data/ceres_data/7vae_31838/03_2025/7vae_31838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vae_31838/03_2025/7vae_31838.cif" } resolution = 3.55 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 39 5.16 5 C 3638 2.51 5 N 909 2.21 5 O 1057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5643 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2290 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1669 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 15, 'TRANS': 205} Chain: "L" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1684 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Time building chain proxies: 4.23, per 1000 atoms: 0.75 Number of scatterers: 5643 At special positions: 0 Unit cell: (90.885, 73.455, 140.685, 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 39 16.00 O 1057 8.00 N 909 7.00 C 3638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 266 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 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: 1.38 Conformation dependent library (CDL) restraints added in 767.5 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1358 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 10 sheets defined 38.3% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 23 through 46 Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.659A pdb=" N ILE A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 84 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.833A pdb=" N ASN A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 removed outlier: 4.127A pdb=" N GLY A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 209 removed outlier: 3.588A pdb=" N VAL A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.846A pdb=" N PHE A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.925A pdb=" N GLY A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.274A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.841A pdb=" N LEU L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 131 Processing helix chain 'L' and resid 190 through 195 removed outlier: 3.813A pdb=" N HIS L 194 " --> pdb=" O GLU L 190 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.706A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TYR H 32 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASN H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.706A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N TYR H 100 " --> pdb=" O PHE H 108 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE H 108 " --> pdb=" O TYR H 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 128 through 132 removed outlier: 4.476A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER H 187 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET H 185 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR H 184 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA H 176 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER H 186 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 161 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.390A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 21 removed outlier: 3.880A pdb=" N VAL L 19 " --> pdb=" O ILE L 81 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE L 81 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 40 through 43 removed outlier: 6.549A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.540A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 158 through 159 287 hydrogen bonds defined for protein. 798 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: 1.54 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1724 1.35 - 1.47: 1453 1.47 - 1.59: 2543 1.59 - 1.71: 0 1.71 - 1.83: 58 Bond restraints: 5778 Sorted by residual: bond pdb=" CB MET A 256 " pdb=" CG MET A 256 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.67e-01 bond pdb=" CB MET A 116 " pdb=" CG MET A 116 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.27e-01 bond pdb=" CA VAL H 191 " pdb=" C VAL H 191 " ideal model delta sigma weight residual 1.524 1.515 0.009 1.05e-02 9.07e+03 8.01e-01 bond pdb=" CB LYS H 151 " pdb=" CG LYS H 151 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.46e-01 bond pdb=" CA ILE H 48 " pdb=" CB ILE H 48 " ideal model delta sigma weight residual 1.545 1.537 0.008 9.10e-03 1.21e+04 7.17e-01 ... (remaining 5773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 7730 2.26 - 4.52: 98 4.52 - 6.78: 17 6.78 - 9.04: 4 9.04 - 11.30: 1 Bond angle restraints: 7850 Sorted by residual: angle pdb=" C ALA H 16 " pdb=" CA ALA H 16 " pdb=" CB ALA H 16 " ideal model delta sigma weight residual 115.89 110.24 5.65 1.32e+00 5.74e-01 1.83e+01 angle pdb=" CA LEU A 150 " pdb=" CB LEU A 150 " pdb=" CG LEU A 150 " ideal model delta sigma weight residual 116.30 127.60 -11.30 3.50e+00 8.16e-02 1.04e+01 angle pdb=" CB MET A 72 " pdb=" CG MET A 72 " pdb=" SD MET A 72 " ideal model delta sigma weight residual 112.70 121.37 -8.67 3.00e+00 1.11e-01 8.36e+00 angle pdb=" CB MET A 256 " pdb=" CG MET A 256 " pdb=" SD MET A 256 " ideal model delta sigma weight residual 112.70 104.69 8.01 3.00e+00 1.11e-01 7.14e+00 angle pdb=" CB LYS H 151 " pdb=" CG LYS H 151 " pdb=" CD LYS H 151 " ideal model delta sigma weight residual 111.30 117.32 -6.02 2.30e+00 1.89e-01 6.84e+00 ... (remaining 7845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3129 17.97 - 35.94: 253 35.94 - 53.91: 50 53.91 - 71.88: 7 71.88 - 89.84: 4 Dihedral angle restraints: 3443 sinusoidal: 1317 harmonic: 2126 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 171.35 -78.35 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CB CYS H 148 " pdb=" SG CYS H 148 " pdb=" SG CYS H 203 " pdb=" CB CYS H 203 " ideal model delta sinusoidal sigma weight residual 93.00 127.11 -34.11 1 1.00e+01 1.00e-02 1.65e+01 dihedral pdb=" CA LEU A 228 " pdb=" C LEU A 228 " pdb=" N MET A 229 " pdb=" CA MET A 229 " ideal model delta harmonic sigma weight residual -180.00 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 3440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 475 0.026 - 0.053: 259 0.053 - 0.079: 101 0.079 - 0.106: 54 0.106 - 0.132: 22 Chirality restraints: 911 Sorted by residual: chirality pdb=" CA THR A 219 " pdb=" N THR A 219 " pdb=" C THR A 219 " pdb=" CB THR A 219 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL H 191 " pdb=" N VAL H 191 " pdb=" C VAL H 191 " pdb=" CB VAL H 191 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.85e-01 chirality pdb=" CA ILE H 104 " pdb=" N ILE H 104 " pdb=" C ILE H 104 " pdb=" CB ILE H 104 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 908 not shown) Planarity restraints: 971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 125 " 0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO H 126 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 57 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.10e+00 pdb=" N PRO A 58 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO A 220 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.027 5.00e-02 4.00e+02 ... (remaining 968 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 602 2.75 - 3.29: 5851 3.29 - 3.82: 9146 3.82 - 4.36: 10288 4.36 - 4.90: 18029 Nonbonded interactions: 43916 Sorted by model distance: nonbonded pdb=" O VAL L 3 " pdb=" OG SER L 26 " model vdw 2.212 3.040 nonbonded pdb=" O VAL A 203 " pdb=" OG SER A 206 " model vdw 2.223 3.040 nonbonded pdb=" O GLY H 8 " pdb=" OG1 THR H 115 " model vdw 2.237 3.040 nonbonded pdb=" NH1 ARG L 160 " pdb=" O ASN L 162 " model vdw 2.283 3.120 nonbonded pdb=" O LEU A 85 " pdb=" NH1 ARG L 33 " model vdw 2.331 3.120 ... (remaining 43911 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.410 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.050 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 21.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 0.035 5778 Z= 0.187 Angle : 0.671 11.300 7850 Z= 0.340 Chirality : 0.042 0.132 911 Planarity : 0.005 0.083 971 Dihedral : 13.730 89.845 2073 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.32), residues: 730 helix: 0.88 (0.34), residues: 237 sheet: 0.38 (0.39), residues: 193 loop : -1.19 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 41 HIS 0.004 0.001 HIS H 35 PHE 0.018 0.001 PHE A 292 TYR 0.022 0.001 TYR H 130 ARG 0.008 0.001 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7448 (mpt-90) cc_final: 0.6778 (mtt180) REVERT: A 27 LEU cc_start: 0.8904 (tt) cc_final: 0.8630 (tt) REVERT: A 31 LEU cc_start: 0.9282 (mm) cc_final: 0.8958 (mm) REVERT: A 32 VAL cc_start: 0.8386 (t) cc_final: 0.7945 (t) REVERT: A 36 LEU cc_start: 0.9075 (mm) cc_final: 0.8712 (mm) REVERT: A 99 SER cc_start: 0.8824 (m) cc_final: 0.8617 (p) REVERT: A 108 PHE cc_start: 0.8213 (m-80) cc_final: 0.7994 (m-10) REVERT: A 128 PHE cc_start: 0.8459 (t80) cc_final: 0.8241 (t80) REVERT: H 130 TYR cc_start: 0.8180 (m-80) cc_final: 0.7304 (m-80) REVERT: H 185 MET cc_start: 0.8801 (ppp) cc_final: 0.8565 (ppp) REVERT: L 42 TYR cc_start: 0.7945 (m-80) cc_final: 0.7574 (m-80) REVERT: L 94 CYS cc_start: 0.6419 (p) cc_final: 0.5440 (p) REVERT: L 162 ASN cc_start: 0.8256 (m-40) cc_final: 0.8042 (m-40) REVERT: L 180 MET cc_start: 0.7604 (tmm) cc_final: 0.6839 (tmm) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1514 time to fit residues: 54.2352 Evaluate side-chains 238 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.0040 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN A 293 GLN L 43 GLN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127599 restraints weight = 10184.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.131333 restraints weight = 4901.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.133716 restraints weight = 2905.323| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5778 Z= 0.236 Angle : 0.690 8.284 7850 Z= 0.349 Chirality : 0.045 0.170 911 Planarity : 0.005 0.063 971 Dihedral : 4.404 19.417 787 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.16 % Favored : 93.70 % Rotamer: Outliers : 2.50 % Allowed : 16.88 % Favored : 80.62 % 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: 0.10 (0.31), residues: 730 helix: 1.23 (0.33), residues: 246 sheet: 0.49 (0.40), residues: 185 loop : -1.19 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 41 HIS 0.002 0.001 HIS L 194 PHE 0.016 0.002 PHE H 174 TYR 0.011 0.001 TYR H 183 ARG 0.004 0.001 ARG L 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 244 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7562 (mpt-90) cc_final: 0.6597 (mtt180) REVERT: A 34 MET cc_start: 0.8763 (ttm) cc_final: 0.8497 (ttm) REVERT: A 36 LEU cc_start: 0.8880 (mm) cc_final: 0.8529 (mm) REVERT: A 82 PHE cc_start: 0.8838 (t80) cc_final: 0.8390 (t80) REVERT: A 117 ASN cc_start: 0.8052 (p0) cc_final: 0.7454 (p0) REVERT: A 128 PHE cc_start: 0.8925 (t80) cc_final: 0.8497 (t80) REVERT: A 189 LYS cc_start: 0.7384 (mmtt) cc_final: 0.6728 (tttm) REVERT: A 292 PHE cc_start: 0.6562 (t80) cc_final: 0.6083 (t80) REVERT: H 36 TRP cc_start: 0.9146 (m100) cc_final: 0.8703 (m100) REVERT: H 56 ASP cc_start: 0.8937 (t0) cc_final: 0.8691 (t0) REVERT: H 73 ASP cc_start: 0.8074 (t0) cc_final: 0.7663 (t0) REVERT: H 130 TYR cc_start: 0.8270 (m-80) cc_final: 0.7561 (m-10) REVERT: H 185 MET cc_start: 0.9012 (ppp) cc_final: 0.8451 (ppp) REVERT: L 17 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7568 (tp30) REVERT: L 41 TRP cc_start: 0.8943 (m100) cc_final: 0.8586 (m100) REVERT: L 42 TYR cc_start: 0.8503 (m-80) cc_final: 0.8127 (m-80) REVERT: L 94 CYS cc_start: 0.6970 (p) cc_final: 0.6499 (p) REVERT: L 180 MET cc_start: 0.8126 (tmm) cc_final: 0.7615 (tmm) REVERT: L 184 LEU cc_start: 0.8954 (mt) cc_final: 0.8699 (mt) REVERT: L 200 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6211 (pm20) REVERT: L 214 PHE cc_start: 0.6311 (t80) cc_final: 0.6030 (t80) outliers start: 16 outliers final: 12 residues processed: 248 average time/residue: 0.1381 time to fit residues: 46.5503 Evaluate side-chains 245 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 232 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 197 TYR Chi-restraints excluded: chain L residue 200 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN H 5 GLN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.151672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124195 restraints weight = 10504.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128012 restraints weight = 4977.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130401 restraints weight = 2933.567| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5778 Z= 0.215 Angle : 0.683 10.746 7850 Z= 0.336 Chirality : 0.045 0.174 911 Planarity : 0.005 0.073 971 Dihedral : 4.426 22.140 787 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.22 % Allowed : 20.31 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.14 (0.31), residues: 730 helix: 1.39 (0.32), residues: 246 sheet: 0.61 (0.40), residues: 183 loop : -1.35 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 168 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.001 PHE H 174 TYR 0.016 0.001 TYR H 50 ARG 0.013 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7549 (mpt-90) cc_final: 0.6630 (mtt180) REVERT: A 34 MET cc_start: 0.8754 (ttm) cc_final: 0.8448 (ttm) REVERT: A 36 LEU cc_start: 0.8978 (mm) cc_final: 0.8584 (mm) REVERT: A 50 LYS cc_start: 0.8327 (mmmm) cc_final: 0.8116 (mmmm) REVERT: A 82 PHE cc_start: 0.8677 (t80) cc_final: 0.8343 (t80) REVERT: A 117 ASN cc_start: 0.8034 (p0) cc_final: 0.7462 (p0) REVERT: A 128 PHE cc_start: 0.8930 (t80) cc_final: 0.8496 (t80) REVERT: A 160 MET cc_start: 0.8423 (mmt) cc_final: 0.7824 (ppp) REVERT: A 292 PHE cc_start: 0.6522 (t80) cc_final: 0.5920 (t80) REVERT: H 5 GLN cc_start: 0.8725 (mm110) cc_final: 0.8447 (mm110) REVERT: H 36 TRP cc_start: 0.9135 (m100) cc_final: 0.8733 (m100) REVERT: H 73 ASP cc_start: 0.8149 (t0) cc_final: 0.7818 (t0) REVERT: H 130 TYR cc_start: 0.8134 (m-80) cc_final: 0.7727 (m-10) REVERT: H 185 MET cc_start: 0.9177 (ppp) cc_final: 0.8545 (ppp) REVERT: L 41 TRP cc_start: 0.9002 (m100) cc_final: 0.8725 (m100) REVERT: L 42 TYR cc_start: 0.8602 (m-80) cc_final: 0.8391 (m-80) REVERT: L 88 ASP cc_start: 0.9142 (m-30) cc_final: 0.8866 (m-30) REVERT: L 96 GLN cc_start: 0.8986 (pp30) cc_final: 0.8663 (pp30) REVERT: L 180 MET cc_start: 0.8155 (tmm) cc_final: 0.7622 (tmm) REVERT: L 200 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6238 (pm20) REVERT: L 214 PHE cc_start: 0.6465 (t80) cc_final: 0.6053 (t80) outliers start: 27 outliers final: 19 residues processed: 251 average time/residue: 0.1317 time to fit residues: 45.2693 Evaluate side-chains 252 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 200 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS A 84 GLN ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 GLN L 27 GLN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.147333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.119896 restraints weight = 10965.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.123554 restraints weight = 5163.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125847 restraints weight = 3048.373| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5778 Z= 0.276 Angle : 0.688 7.854 7850 Z= 0.345 Chirality : 0.045 0.147 911 Planarity : 0.005 0.059 971 Dihedral : 4.571 22.383 787 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 5.47 % Allowed : 22.50 % Favored : 72.03 % 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: -0.04 (0.31), residues: 730 helix: 1.23 (0.32), residues: 247 sheet: 0.39 (0.38), residues: 196 loop : -1.44 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 168 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.001 PHE H 154 TYR 0.016 0.002 TYR L 145 ARG 0.008 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7514 (mpt-90) cc_final: 0.6667 (mtt180) REVERT: A 34 MET cc_start: 0.8769 (ttm) cc_final: 0.8408 (ttm) REVERT: A 36 LEU cc_start: 0.8956 (mm) cc_final: 0.8546 (mm) REVERT: A 50 LYS cc_start: 0.8260 (mmmm) cc_final: 0.8052 (mmmm) REVERT: A 82 PHE cc_start: 0.8789 (t80) cc_final: 0.8415 (t80) REVERT: A 116 MET cc_start: 0.7628 (tpp) cc_final: 0.7375 (tpp) REVERT: A 117 ASN cc_start: 0.8147 (p0) cc_final: 0.7601 (p0) REVERT: A 160 MET cc_start: 0.8382 (mmt) cc_final: 0.7853 (ppp) REVERT: H 5 GLN cc_start: 0.8682 (mm110) cc_final: 0.8403 (mm110) REVERT: H 36 TRP cc_start: 0.9154 (m100) cc_final: 0.8686 (m100) REVERT: H 73 ASP cc_start: 0.8301 (t0) cc_final: 0.7916 (t0) REVERT: H 179 GLN cc_start: 0.8499 (pp30) cc_final: 0.8079 (pp30) REVERT: H 185 MET cc_start: 0.9141 (ppp) cc_final: 0.8477 (ppp) REVERT: L 41 TRP cc_start: 0.9047 (m100) cc_final: 0.8742 (m100) REVERT: L 42 TYR cc_start: 0.8818 (m-80) cc_final: 0.8598 (m-80) REVERT: L 96 GLN cc_start: 0.9056 (pp30) cc_final: 0.8582 (pp30) REVERT: L 121 SER cc_start: 0.8631 (m) cc_final: 0.8415 (t) REVERT: L 180 MET cc_start: 0.8222 (tmm) cc_final: 0.7569 (tmm) REVERT: L 200 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6367 (pm20) REVERT: L 214 PHE cc_start: 0.6777 (t80) cc_final: 0.6377 (t80) outliers start: 35 outliers final: 30 residues processed: 255 average time/residue: 0.1344 time to fit residues: 47.2136 Evaluate side-chains 265 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 200 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS A 86 ASN A 293 GLN H 113 GLN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.148759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121365 restraints weight = 10824.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.125124 restraints weight = 5092.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127549 restraints weight = 2977.168| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5778 Z= 0.212 Angle : 0.683 8.759 7850 Z= 0.335 Chirality : 0.044 0.146 911 Planarity : 0.004 0.055 971 Dihedral : 4.478 22.657 787 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 5.16 % Allowed : 25.16 % Favored : 69.69 % 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: 0.01 (0.31), residues: 730 helix: 1.29 (0.32), residues: 247 sheet: 0.50 (0.39), residues: 194 loop : -1.49 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 168 HIS 0.004 0.001 HIS L 194 PHE 0.012 0.001 PHE H 154 TYR 0.020 0.001 TYR L 145 ARG 0.006 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7399 (mpt-90) cc_final: 0.6664 (mtt180) REVERT: A 34 MET cc_start: 0.8745 (ttm) cc_final: 0.8384 (ttm) REVERT: A 36 LEU cc_start: 0.8924 (mm) cc_final: 0.8516 (mm) REVERT: A 82 PHE cc_start: 0.8785 (t80) cc_final: 0.8403 (t80) REVERT: A 117 ASN cc_start: 0.8254 (p0) cc_final: 0.7741 (p0) REVERT: H 5 GLN cc_start: 0.8664 (mm110) cc_final: 0.8304 (mm110) REVERT: H 73 ASP cc_start: 0.8272 (t0) cc_final: 0.7973 (t70) REVERT: H 179 GLN cc_start: 0.8577 (pp30) cc_final: 0.8175 (pp30) REVERT: H 185 MET cc_start: 0.9204 (ppp) cc_final: 0.8578 (ppp) REVERT: L 41 TRP cc_start: 0.9045 (m100) cc_final: 0.8747 (m100) REVERT: L 42 TYR cc_start: 0.8776 (m-80) cc_final: 0.8513 (m-80) REVERT: L 121 SER cc_start: 0.8454 (m) cc_final: 0.8171 (t) REVERT: L 200 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6619 (pm20) REVERT: L 214 PHE cc_start: 0.6822 (t80) cc_final: 0.6597 (t80) outliers start: 33 outliers final: 27 residues processed: 256 average time/residue: 0.1319 time to fit residues: 46.1996 Evaluate side-chains 261 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 200 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 26 optimal weight: 0.0010 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN H 113 GLN L 27 GLN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.149034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121840 restraints weight = 10818.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125572 restraints weight = 5097.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.127920 restraints weight = 2977.447| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5778 Z= 0.208 Angle : 0.677 8.492 7850 Z= 0.332 Chirality : 0.044 0.143 911 Planarity : 0.005 0.057 971 Dihedral : 4.487 23.767 787 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 5.78 % Allowed : 24.84 % Favored : 69.38 % 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: 0.03 (0.32), residues: 730 helix: 1.38 (0.33), residues: 247 sheet: 0.51 (0.39), residues: 193 loop : -1.55 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 162 HIS 0.004 0.001 HIS H 35 PHE 0.017 0.001 PHE H 154 TYR 0.020 0.001 TYR L 145 ARG 0.007 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7499 (mpt-90) cc_final: 0.6679 (mtt180) REVERT: A 34 MET cc_start: 0.8743 (ttm) cc_final: 0.8397 (ttm) REVERT: A 36 LEU cc_start: 0.8934 (mm) cc_final: 0.8543 (mm) REVERT: A 82 PHE cc_start: 0.8776 (t80) cc_final: 0.8419 (t80) REVERT: A 93 ILE cc_start: 0.9128 (tp) cc_final: 0.8900 (tp) REVERT: A 117 ASN cc_start: 0.8355 (p0) cc_final: 0.7749 (p0) REVERT: A 160 MET cc_start: 0.8374 (mmt) cc_final: 0.8118 (mmp) REVERT: A 283 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8272 (m-80) REVERT: H 73 ASP cc_start: 0.8276 (t0) cc_final: 0.7999 (t0) REVERT: H 146 LEU cc_start: 0.9421 (mt) cc_final: 0.9131 (mt) REVERT: H 179 GLN cc_start: 0.8671 (pp30) cc_final: 0.8380 (pp30) REVERT: H 185 MET cc_start: 0.9242 (ppp) cc_final: 0.8563 (ppp) REVERT: L 41 TRP cc_start: 0.9056 (m100) cc_final: 0.8688 (m100) REVERT: L 42 TYR cc_start: 0.8781 (m-80) cc_final: 0.8486 (m-80) REVERT: L 96 GLN cc_start: 0.9065 (pp30) cc_final: 0.8662 (pp30) REVERT: L 200 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6595 (pm20) REVERT: L 214 PHE cc_start: 0.6813 (t80) cc_final: 0.6606 (t80) outliers start: 37 outliers final: 30 residues processed: 256 average time/residue: 0.1274 time to fit residues: 44.8205 Evaluate side-chains 272 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 200 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN H 113 GLN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 HIS ** 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 = 0.3889 r_free = 0.3889 target = 0.148429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.120993 restraints weight = 10967.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124734 restraints weight = 5169.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127085 restraints weight = 3024.430| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5778 Z= 0.220 Angle : 0.703 8.462 7850 Z= 0.343 Chirality : 0.045 0.160 911 Planarity : 0.005 0.059 971 Dihedral : 4.489 25.509 787 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 5.62 % Allowed : 25.62 % Favored : 68.75 % 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: 0.09 (0.32), residues: 730 helix: 1.53 (0.33), residues: 248 sheet: 0.48 (0.39), residues: 193 loop : -1.58 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 162 HIS 0.004 0.001 HIS H 35 PHE 0.016 0.001 PHE H 154 TYR 0.021 0.001 TYR L 145 ARG 0.007 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7432 (mpt-90) cc_final: 0.6667 (mtt180) REVERT: A 34 MET cc_start: 0.8779 (ttm) cc_final: 0.8429 (ttm) REVERT: A 36 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8544 (mm) REVERT: A 82 PHE cc_start: 0.8779 (t80) cc_final: 0.8415 (t80) REVERT: A 89 GLU cc_start: 0.8086 (mp0) cc_final: 0.7776 (mp0) REVERT: A 93 ILE cc_start: 0.9124 (tp) cc_final: 0.8908 (tp) REVERT: A 116 MET cc_start: 0.7779 (tpp) cc_final: 0.7508 (tpp) REVERT: A 117 ASN cc_start: 0.8346 (p0) cc_final: 0.7895 (p0) REVERT: A 160 MET cc_start: 0.8343 (mmt) cc_final: 0.8097 (mmp) REVERT: A 283 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: H 47 TRP cc_start: 0.9070 (t60) cc_final: 0.8364 (t60) REVERT: H 73 ASP cc_start: 0.8314 (t0) cc_final: 0.8031 (t70) REVERT: H 146 LEU cc_start: 0.9419 (mt) cc_final: 0.9133 (mt) REVERT: H 179 GLN cc_start: 0.8701 (pp30) cc_final: 0.8390 (pp30) REVERT: H 185 MET cc_start: 0.9230 (ppp) cc_final: 0.8539 (ppp) REVERT: L 41 TRP cc_start: 0.9069 (m100) cc_final: 0.8680 (m100) REVERT: L 200 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6627 (pm20) outliers start: 36 outliers final: 29 residues processed: 252 average time/residue: 0.1285 time to fit residues: 44.5364 Evaluate side-chains 262 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 200 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 22 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.144969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117980 restraints weight = 10758.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121473 restraints weight = 5087.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123803 restraints weight = 2981.999| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5778 Z= 0.275 Angle : 0.731 8.982 7850 Z= 0.358 Chirality : 0.046 0.174 911 Planarity : 0.005 0.060 971 Dihedral : 4.679 29.384 787 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 6.25 % Allowed : 25.94 % Favored : 67.81 % 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: -0.01 (0.31), residues: 730 helix: 1.55 (0.33), residues: 247 sheet: 0.10 (0.40), residues: 180 loop : -1.40 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 162 HIS 0.003 0.001 HIS H 35 PHE 0.024 0.001 PHE A 292 TYR 0.022 0.002 TYR L 145 ARG 0.008 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7436 (mpt-90) cc_final: 0.6688 (mtt180) REVERT: A 34 MET cc_start: 0.8732 (ttm) cc_final: 0.8362 (ttm) REVERT: A 36 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8594 (mm) REVERT: A 82 PHE cc_start: 0.8823 (t80) cc_final: 0.8446 (t80) REVERT: A 93 ILE cc_start: 0.9119 (tp) cc_final: 0.8910 (tp) REVERT: A 116 MET cc_start: 0.7957 (tpp) cc_final: 0.7752 (tpp) REVERT: A 117 ASN cc_start: 0.8489 (p0) cc_final: 0.7771 (p0) REVERT: A 160 MET cc_start: 0.8436 (mmt) cc_final: 0.8190 (mmp) REVERT: A 283 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: H 54 TYR cc_start: 0.8781 (t80) cc_final: 0.8569 (t80) REVERT: H 73 ASP cc_start: 0.8258 (t0) cc_final: 0.7953 (t70) REVERT: H 146 LEU cc_start: 0.9402 (mt) cc_final: 0.9145 (mt) REVERT: H 179 GLN cc_start: 0.8609 (pp30) cc_final: 0.8159 (pp30) REVERT: H 185 MET cc_start: 0.9235 (ppp) cc_final: 0.8568 (ppp) REVERT: L 41 TRP cc_start: 0.9198 (m100) cc_final: 0.8740 (m100) REVERT: L 61 GLU cc_start: 0.9123 (tp30) cc_final: 0.8220 (tm-30) REVERT: L 123 PHE cc_start: 0.8042 (m-80) cc_final: 0.7646 (m-80) REVERT: L 162 ASN cc_start: 0.8515 (m-40) cc_final: 0.8312 (m110) REVERT: L 200 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6666 (pm20) outliers start: 40 outliers final: 34 residues processed: 250 average time/residue: 0.1358 time to fit residues: 46.7608 Evaluate side-chains 278 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 200 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 0.0040 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 0.0010 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.148652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121813 restraints weight = 10804.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125447 restraints weight = 5096.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.127776 restraints weight = 2968.468| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5778 Z= 0.202 Angle : 0.738 9.095 7850 Z= 0.354 Chirality : 0.045 0.158 911 Planarity : 0.004 0.062 971 Dihedral : 4.558 29.289 787 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.84 % Allowed : 29.22 % Favored : 65.94 % 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: 0.06 (0.32), residues: 730 helix: 1.59 (0.32), residues: 248 sheet: 0.41 (0.40), residues: 190 loop : -1.62 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 162 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.001 PHE H 154 TYR 0.024 0.001 TYR L 145 ARG 0.007 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7487 (mpt-90) cc_final: 0.6703 (mtt180) REVERT: A 34 MET cc_start: 0.8741 (ttm) cc_final: 0.8368 (ttm) REVERT: A 36 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8596 (mm) REVERT: A 58 PRO cc_start: 0.8276 (Cg_endo) cc_final: 0.7903 (Cg_exo) REVERT: A 82 PHE cc_start: 0.8756 (t80) cc_final: 0.8430 (t80) REVERT: A 89 GLU cc_start: 0.8171 (mp0) cc_final: 0.7858 (mp0) REVERT: A 116 MET cc_start: 0.7864 (tpp) cc_final: 0.7571 (tpp) REVERT: A 117 ASN cc_start: 0.8338 (p0) cc_final: 0.7914 (p0) REVERT: A 160 MET cc_start: 0.8383 (mmt) cc_final: 0.8154 (mmp) REVERT: A 283 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8293 (m-80) REVERT: H 54 TYR cc_start: 0.8683 (t80) cc_final: 0.8463 (t80) REVERT: H 73 ASP cc_start: 0.8208 (t0) cc_final: 0.7800 (t0) REVERT: H 146 LEU cc_start: 0.9422 (mt) cc_final: 0.9156 (mt) REVERT: H 179 GLN cc_start: 0.8631 (pp30) cc_final: 0.8202 (pp30) REVERT: H 185 MET cc_start: 0.9236 (ppp) cc_final: 0.8544 (ppp) REVERT: L 41 TRP cc_start: 0.9118 (m100) cc_final: 0.8653 (m100) REVERT: L 61 GLU cc_start: 0.9076 (tp30) cc_final: 0.8202 (tm-30) REVERT: L 107 THR cc_start: 0.9264 (m) cc_final: 0.9000 (t) REVERT: L 123 PHE cc_start: 0.7891 (m-80) cc_final: 0.7448 (m-80) REVERT: L 200 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6875 (pm20) outliers start: 31 outliers final: 26 residues processed: 247 average time/residue: 0.1238 time to fit residues: 42.3012 Evaluate side-chains 264 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 200 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 50 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.147554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120459 restraints weight = 10945.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.124101 restraints weight = 5143.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.126327 restraints weight = 3002.838| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5778 Z= 0.221 Angle : 0.770 11.625 7850 Z= 0.362 Chirality : 0.046 0.226 911 Planarity : 0.004 0.060 971 Dihedral : 4.634 32.131 787 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 5.16 % Allowed : 29.69 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.02 (0.31), residues: 730 helix: 1.59 (0.32), residues: 248 sheet: 0.36 (0.40), residues: 191 loop : -1.67 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 162 HIS 0.004 0.001 HIS H 35 PHE 0.016 0.001 PHE H 154 TYR 0.022 0.001 TYR L 145 ARG 0.007 0.000 ARG A 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7374 (mpt-90) cc_final: 0.6597 (mtt180) REVERT: A 34 MET cc_start: 0.8745 (ttm) cc_final: 0.8358 (ttm) REVERT: A 36 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8594 (mm) REVERT: A 58 PRO cc_start: 0.8361 (Cg_endo) cc_final: 0.7981 (Cg_exo) REVERT: A 82 PHE cc_start: 0.8756 (t80) cc_final: 0.8426 (t80) REVERT: A 116 MET cc_start: 0.7856 (tpp) cc_final: 0.7639 (tpp) REVERT: A 117 ASN cc_start: 0.8472 (p0) cc_final: 0.7697 (p0) REVERT: A 160 MET cc_start: 0.8400 (mmt) cc_final: 0.8172 (mmp) REVERT: A 283 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: H 47 TRP cc_start: 0.9051 (t60) cc_final: 0.8406 (t60) REVERT: H 54 TYR cc_start: 0.8691 (t80) cc_final: 0.8473 (t80) REVERT: H 73 ASP cc_start: 0.8109 (t0) cc_final: 0.7731 (t0) REVERT: H 146 LEU cc_start: 0.9434 (mt) cc_final: 0.9167 (mt) REVERT: H 179 GLN cc_start: 0.8646 (pp30) cc_final: 0.7864 (pm20) REVERT: H 185 MET cc_start: 0.9221 (ppp) cc_final: 0.8518 (ppp) REVERT: L 41 TRP cc_start: 0.9148 (m100) cc_final: 0.8661 (m100) REVERT: L 61 GLU cc_start: 0.9088 (tp30) cc_final: 0.8412 (tm-30) REVERT: L 107 THR cc_start: 0.9306 (m) cc_final: 0.8972 (t) REVERT: L 123 PHE cc_start: 0.7903 (m-80) cc_final: 0.7458 (m-80) REVERT: L 200 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6725 (pm20) outliers start: 33 outliers final: 24 residues processed: 250 average time/residue: 0.1271 time to fit residues: 43.5537 Evaluate side-chains 265 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 200 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 57 optimal weight: 0.0570 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.147847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120808 restraints weight = 10931.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124468 restraints weight = 5122.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.126825 restraints weight = 2981.333| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5778 Z= 0.214 Angle : 0.768 11.687 7850 Z= 0.365 Chirality : 0.046 0.208 911 Planarity : 0.005 0.062 971 Dihedral : 4.608 32.409 787 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.38 % Allowed : 31.25 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.03 (0.31), residues: 730 helix: 1.63 (0.32), residues: 248 sheet: 0.38 (0.40), residues: 191 loop : -1.72 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 168 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.001 PHE H 154 TYR 0.022 0.001 TYR L 145 ARG 0.007 0.000 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2214.09 seconds wall clock time: 39 minutes 9.63 seconds (2349.63 seconds total)