Starting phenix.real_space_refine on Fri Dec 27 15:21:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vae_31838/12_2024/7vae_31838.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vae_31838/12_2024/7vae_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_31838/12_2024/7vae_31838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vae_31838/12_2024/7vae_31838.map" model { file = "/net/cci-nas-00/data/ceres_data/7vae_31838/12_2024/7vae_31838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vae_31838/12_2024/7vae_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-5532/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: 3.86, per 1000 atoms: 0.68 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: 1.31 Conformation dependent library (CDL) restraints added in 647.0 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: 0.58 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: 1.43 Time building geometry restraints manager: 1.53 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.390 Find NCS groups from input model: 0.050 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.960 ------------------------------------------------------------------------------- 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 : 0.641 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: 0.1502 time to fit residues: 53.6732 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 : 0.655 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7290 (mpt-90) cc_final: 0.6496 (mtt180) REVERT: A 36 LEU cc_start: 0.9113 (mm) cc_final: 0.8771 (mm) REVERT: A 117 ASN cc_start: 0.7992 (p0) cc_final: 0.7590 (p0) REVERT: A 189 LYS cc_start: 0.7697 (mmtt) cc_final: 0.6822 (tttm) REVERT: H 130 TYR cc_start: 0.8113 (m-80) cc_final: 0.7330 (m-10) REVERT: H 185 MET cc_start: 0.8991 (ppp) cc_final: 0.8698 (ppp) REVERT: L 94 CYS cc_start: 0.6751 (p) cc_final: 0.6493 (p) REVERT: L 180 MET cc_start: 0.7773 (tmm) cc_final: 0.7502 (tmm) REVERT: L 184 LEU cc_start: 0.9022 (mt) cc_final: 0.8768 (mt) REVERT: L 200 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6447 (pm20) outliers start: 16 outliers final: 12 residues processed: 248 average time/residue: 0.1436 time to fit residues: 48.1174 Evaluate side-chains 244 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 231 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 36 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5778 Z= 0.254 Angle : 0.696 10.106 7850 Z= 0.347 Chirality : 0.045 0.170 911 Planarity : 0.005 0.067 971 Dihedral : 4.522 22.386 787 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.69 % Allowed : 20.00 % Favored : 75.31 % 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: 0.05 (0.31), residues: 730 helix: 1.29 (0.32), residues: 247 sheet: 0.55 (0.39), residues: 188 loop : -1.42 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP L 41 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.002 PHE H 174 TYR 0.017 0.002 TYR L 197 ARG 0.010 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 275 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7299 (mpt-90) cc_final: 0.6591 (mtt180) REVERT: A 34 MET cc_start: 0.8041 (ttm) cc_final: 0.7839 (ttm) REVERT: A 36 LEU cc_start: 0.9117 (mm) cc_final: 0.8763 (mm) REVERT: A 116 MET cc_start: 0.7436 (tpp) cc_final: 0.7179 (tpp) REVERT: A 117 ASN cc_start: 0.7960 (p0) cc_final: 0.7555 (p0) REVERT: A 138 LEU cc_start: 0.9534 (mt) cc_final: 0.9283 (mt) REVERT: H 113 GLN cc_start: 0.8084 (pt0) cc_final: 0.7767 (pt0) REVERT: H 130 TYR cc_start: 0.7990 (m-80) cc_final: 0.7501 (m-10) REVERT: H 151 LYS cc_start: 0.8285 (tppt) cc_final: 0.8015 (tppp) REVERT: H 185 MET cc_start: 0.9103 (ppp) cc_final: 0.8716 (ppp) REVERT: L 180 MET cc_start: 0.7787 (tmm) cc_final: 0.7513 (tmm) REVERT: L 200 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6547 (pm20) outliers start: 30 outliers final: 22 residues processed: 254 average time/residue: 0.1396 time to fit residues: 47.8232 Evaluate side-chains 243 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 187 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 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 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 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 64 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 0.0570 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2975 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= 0.209 Angle : 0.678 9.047 7850 Z= 0.337 Chirality : 0.044 0.150 911 Planarity : 0.005 0.058 971 Dihedral : 4.524 23.906 787 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.06 % Allowed : 23.91 % 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: 1.18 (0.32), residues: 248 sheet: 0.52 (0.39), residues: 188 loop : -1.45 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP L 41 HIS 0.004 0.001 HIS L 194 PHE 0.017 0.001 PHE A 82 TYR 0.018 0.001 TYR L 145 ARG 0.007 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 271 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8113 (m-80) cc_final: 0.7480 (t80) REVERT: A 25 ARG cc_start: 0.7209 (mpt-90) cc_final: 0.6613 (mtt180) REVERT: A 34 MET cc_start: 0.8023 (ttm) cc_final: 0.7806 (ttm) REVERT: A 36 LEU cc_start: 0.9055 (mm) cc_final: 0.8669 (mm) REVERT: A 117 ASN cc_start: 0.7968 (p0) cc_final: 0.7689 (p0) REVERT: H 113 GLN cc_start: 0.8005 (pt0) cc_final: 0.7727 (pt0) REVERT: H 130 TYR cc_start: 0.7939 (m-80) cc_final: 0.7483 (m-10) REVERT: H 179 GLN cc_start: 0.8328 (pp30) cc_final: 0.8059 (pp30) REVERT: H 185 MET cc_start: 0.9065 (ppp) cc_final: 0.8746 (ppp) REVERT: L 121 SER cc_start: 0.8606 (m) cc_final: 0.8343 (t) REVERT: L 144 PHE cc_start: 0.8008 (p90) cc_final: 0.7722 (p90) REVERT: L 200 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6511 (pm20) outliers start: 26 outliers final: 23 residues processed: 255 average time/residue: 0.1325 time to fit residues: 46.0944 Evaluate side-chains 255 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 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 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 218 LEU Chi-restraints excluded: chain L residue 3 VAL 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 182 SER 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 57 optimal weight: 0.7980 chunk 39 optimal weight: 0.0050 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3161 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= 0.205 Angle : 0.684 9.272 7850 Z= 0.335 Chirality : 0.044 0.147 911 Planarity : 0.004 0.055 971 Dihedral : 4.439 22.127 787 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.31 % Allowed : 25.62 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.29 (0.33), residues: 248 sheet: 0.44 (0.39), residues: 194 loop : -1.55 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 41 HIS 0.003 0.001 HIS L 194 PHE 0.015 0.001 PHE A 82 TYR 0.019 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 269 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7835 (p0) REVERT: A 25 ARG cc_start: 0.7074 (mpt-90) cc_final: 0.6496 (mtt180) REVERT: A 34 MET cc_start: 0.8011 (ttm) cc_final: 0.7798 (ttm) REVERT: A 36 LEU cc_start: 0.9058 (mm) cc_final: 0.8654 (mm) REVERT: A 117 ASN cc_start: 0.8002 (p0) cc_final: 0.7697 (p0) REVERT: H 113 GLN cc_start: 0.7982 (pt0) cc_final: 0.7715 (pt0) REVERT: H 185 MET cc_start: 0.9096 (ppp) cc_final: 0.8722 (ppp) REVERT: L 121 SER cc_start: 0.8603 (m) cc_final: 0.8368 (t) REVERT: L 200 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6617 (pm20) outliers start: 34 outliers final: 25 residues processed: 245 average time/residue: 0.1257 time to fit residues: 42.8433 Evaluate side-chains 255 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP 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 270 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.0170 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 17 optimal weight: 0.0970 chunk 69 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS A 293 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5778 Z= 0.188 Angle : 0.671 7.756 7850 Z= 0.329 Chirality : 0.044 0.146 911 Planarity : 0.005 0.057 971 Dihedral : 4.433 23.753 787 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.53 % Allowed : 26.56 % Favored : 68.91 % 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: -0.00 (0.31), residues: 730 helix: 1.38 (0.33), residues: 248 sheet: 0.45 (0.39), residues: 193 loop : -1.58 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 41 HIS 0.004 0.001 HIS H 35 PHE 0.016 0.001 PHE H 154 TYR 0.020 0.001 TYR L 145 ARG 0.005 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 264 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7696 (p0) REVERT: A 25 ARG cc_start: 0.7092 (mpt-90) cc_final: 0.6607 (mtt180) REVERT: A 34 MET cc_start: 0.7975 (ttm) cc_final: 0.7771 (ttm) REVERT: A 36 LEU cc_start: 0.9062 (mm) cc_final: 0.8656 (mm) REVERT: A 117 ASN cc_start: 0.8044 (p0) cc_final: 0.7662 (p0) REVERT: H 113 GLN cc_start: 0.7972 (pt0) cc_final: 0.7700 (pt0) REVERT: H 179 GLN cc_start: 0.8503 (pp30) cc_final: 0.8279 (pp30) REVERT: H 185 MET cc_start: 0.9074 (ppp) cc_final: 0.8687 (ppp) REVERT: L 121 SER cc_start: 0.8642 (m) cc_final: 0.8390 (t) REVERT: L 144 PHE cc_start: 0.8077 (p90) cc_final: 0.7762 (p90) outliers start: 29 outliers final: 23 residues processed: 247 average time/residue: 0.1432 time to fit residues: 48.2728 Evaluate side-chains 247 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 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 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 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 110 GLU Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 165 LEU 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 7 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.0670 overall best weight: 0.9122 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5778 Z= 0.235 Angle : 0.699 8.734 7850 Z= 0.344 Chirality : 0.045 0.170 911 Planarity : 0.004 0.059 971 Dihedral : 4.484 27.733 787 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 5.78 % Allowed : 25.94 % Favored : 68.28 % 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: 0.05 (0.31), residues: 730 helix: 1.55 (0.33), residues: 248 sheet: 0.34 (0.38), residues: 193 loop : -1.56 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 41 HIS 0.006 0.001 HIS A 221 PHE 0.023 0.001 PHE A 82 TYR 0.021 0.001 TYR L 145 ARG 0.006 0.001 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 269 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7734 (p0) REVERT: A 25 ARG cc_start: 0.7159 (mpt-90) cc_final: 0.6679 (mtt180) REVERT: A 36 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8679 (mm) REVERT: A 116 MET cc_start: 0.7616 (tpp) cc_final: 0.7352 (tpp) REVERT: A 117 ASN cc_start: 0.8154 (p0) cc_final: 0.7933 (p0) REVERT: A 189 LYS cc_start: 0.7395 (mmtt) cc_final: 0.6030 (pttt) REVERT: A 222 LEU cc_start: 0.7985 (mt) cc_final: 0.7649 (tp) REVERT: A 229 MET cc_start: 0.7885 (tpp) cc_final: 0.7618 (tpp) REVERT: A 283 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.7954 (m-80) REVERT: H 113 GLN cc_start: 0.7975 (pt0) cc_final: 0.7704 (pt0) REVERT: H 146 LEU cc_start: 0.9159 (mt) cc_final: 0.8876 (mt) REVERT: H 179 GLN cc_start: 0.8568 (pp30) cc_final: 0.8309 (pp30) REVERT: H 185 MET cc_start: 0.9091 (ppp) cc_final: 0.8682 (ppp) REVERT: L 200 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6412 (pm20) outliers start: 37 outliers final: 30 residues processed: 246 average time/residue: 0.1333 time to fit residues: 45.2215 Evaluate side-chains 262 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 122 MET 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 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 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 97 SER 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 165 LEU 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 20 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3620 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= 0.213 Angle : 0.727 8.592 7850 Z= 0.351 Chirality : 0.045 0.187 911 Planarity : 0.005 0.064 971 Dihedral : 4.572 26.513 787 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.31 % Allowed : 27.50 % Favored : 67.19 % 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: 0.05 (0.31), residues: 730 helix: 1.53 (0.33), residues: 248 sheet: 0.39 (0.39), residues: 190 loop : -1.56 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 41 HIS 0.005 0.001 HIS A 221 PHE 0.021 0.001 PHE A 82 TYR 0.023 0.001 TYR L 145 ARG 0.006 0.000 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 265 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7674 (p0) REVERT: A 25 ARG cc_start: 0.7140 (mpt-90) cc_final: 0.6697 (mtt180) REVERT: A 36 LEU cc_start: 0.9067 (mm) cc_final: 0.8801 (mm) REVERT: A 93 ILE cc_start: 0.9283 (tp) cc_final: 0.9003 (tp) REVERT: A 117 ASN cc_start: 0.8249 (p0) cc_final: 0.7737 (p0) REVERT: A 283 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: H 47 TRP cc_start: 0.8801 (t60) cc_final: 0.8274 (t60) REVERT: H 113 GLN cc_start: 0.7972 (pt0) cc_final: 0.7704 (pt0) REVERT: H 146 LEU cc_start: 0.9151 (mt) cc_final: 0.8876 (mt) REVERT: H 179 GLN cc_start: 0.8599 (pp30) cc_final: 0.8355 (pp30) REVERT: H 185 MET cc_start: 0.9090 (ppp) cc_final: 0.8679 (ppp) REVERT: L 61 GLU cc_start: 0.8482 (tp30) cc_final: 0.8184 (tm-30) REVERT: L 200 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6660 (pm20) outliers start: 34 outliers final: 30 residues processed: 243 average time/residue: 0.1371 time to fit residues: 45.7025 Evaluate side-chains 256 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 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 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 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 11 LEU Chi-restraints excluded: chain L residue 19 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 165 LEU 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 66 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 42 optimal weight: 0.0670 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 0.0970 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5778 Z= 0.199 Angle : 0.748 8.885 7850 Z= 0.359 Chirality : 0.045 0.193 911 Planarity : 0.005 0.061 971 Dihedral : 4.561 30.883 787 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.69 % Allowed : 29.06 % Favored : 66.25 % 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: 0.07 (0.31), residues: 730 helix: 1.59 (0.33), residues: 248 sheet: 0.39 (0.39), residues: 190 loop : -1.59 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 162 HIS 0.003 0.001 HIS A 221 PHE 0.020 0.001 PHE A 82 TYR 0.021 0.001 TYR L 145 ARG 0.006 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 256 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7591 (p0) REVERT: A 25 ARG cc_start: 0.7123 (mpt-90) cc_final: 0.6679 (mtt180) REVERT: A 36 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8644 (mm) REVERT: A 93 ILE cc_start: 0.9267 (tp) cc_final: 0.9029 (tp) REVERT: A 116 MET cc_start: 0.7576 (tpp) cc_final: 0.7275 (tpp) REVERT: A 117 ASN cc_start: 0.8118 (p0) cc_final: 0.7689 (p0) REVERT: A 139 TYR cc_start: 0.9100 (t80) cc_final: 0.8884 (t80) REVERT: H 54 TYR cc_start: 0.7864 (t80) cc_final: 0.7640 (t80) REVERT: H 113 GLN cc_start: 0.7929 (pt0) cc_final: 0.7649 (pt0) REVERT: H 146 LEU cc_start: 0.9138 (mt) cc_final: 0.8867 (mt) REVERT: H 179 GLN cc_start: 0.8562 (pp30) cc_final: 0.8327 (pp30) REVERT: H 185 MET cc_start: 0.9061 (ppp) cc_final: 0.8621 (ppp) REVERT: L 61 GLU cc_start: 0.8500 (tp30) cc_final: 0.8261 (tm-30) REVERT: L 200 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6451 (pm20) outliers start: 30 outliers final: 27 residues processed: 236 average time/residue: 0.1305 time to fit residues: 42.3866 Evaluate side-chains 251 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP 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 140 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 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 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 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 165 LEU 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 32 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5778 Z= 0.246 Angle : 0.769 11.132 7850 Z= 0.370 Chirality : 0.046 0.212 911 Planarity : 0.005 0.064 971 Dihedral : 4.639 30.557 787 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 5.00 % Allowed : 29.38 % Favored : 65.62 % 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: -0.01 (0.31), residues: 730 helix: 1.58 (0.33), residues: 247 sheet: 0.27 (0.38), residues: 191 loop : -1.63 (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 A 221 PHE 0.020 0.001 PHE A 82 TYR 0.022 0.002 TYR L 145 ARG 0.006 0.001 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 257 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7678 (p0) REVERT: A 25 ARG cc_start: 0.7112 (mpt-90) cc_final: 0.6701 (mtt180) REVERT: A 93 ILE cc_start: 0.9300 (tp) cc_final: 0.9035 (tp) REVERT: A 116 MET cc_start: 0.7522 (tpp) cc_final: 0.7174 (tpp) REVERT: A 117 ASN cc_start: 0.8179 (p0) cc_final: 0.7643 (p0) REVERT: A 139 TYR cc_start: 0.9116 (t80) cc_final: 0.8895 (t80) REVERT: A 283 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7897 (m-80) REVERT: H 54 TYR cc_start: 0.7945 (t80) cc_final: 0.7693 (t80) REVERT: H 113 GLN cc_start: 0.7923 (pt0) cc_final: 0.7651 (pt0) REVERT: H 146 LEU cc_start: 0.9179 (mt) cc_final: 0.8915 (mt) REVERT: H 179 GLN cc_start: 0.8688 (pp30) cc_final: 0.8450 (pp30) REVERT: H 185 MET cc_start: 0.9101 (ppp) cc_final: 0.8683 (ppp) REVERT: L 61 GLU cc_start: 0.8540 (tp30) cc_final: 0.8171 (tm-30) REVERT: L 123 PHE cc_start: 0.7852 (m-80) cc_final: 0.7544 (m-80) REVERT: L 200 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6874 (pm20) outliers start: 32 outliers final: 26 residues processed: 237 average time/residue: 0.1324 time to fit residues: 43.1692 Evaluate side-chains 254 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 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 270 LEU Chi-restraints excluded: chain A residue 283 PHE 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 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 140 PHE Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 165 LEU 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 52 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 0.0030 chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 = 0.148482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121853 restraints weight = 10848.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125473 restraints weight = 5093.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.127809 restraints weight = 2977.263| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5778 Z= 0.227 Angle : 0.790 11.766 7850 Z= 0.375 Chirality : 0.047 0.227 911 Planarity : 0.004 0.062 971 Dihedral : 4.608 30.982 787 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 5.00 % Allowed : 30.16 % Favored : 64.84 % 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: -0.08 (0.31), residues: 730 helix: 1.49 (0.33), residues: 249 sheet: 0.29 (0.39), residues: 191 loop : -1.70 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 41 HIS 0.004 0.001 HIS A 221 PHE 0.020 0.001 PHE A 82 TYR 0.024 0.001 TYR L 145 ARG 0.006 0.000 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1667.35 seconds wall clock time: 31 minutes 4.76 seconds (1864.76 seconds total)