Starting phenix.real_space_refine on Tue Feb 13 11:10:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vae_31838/02_2024/7vae_31838.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vae_31838/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vae_31838/02_2024/7vae_31838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vae_31838/02_2024/7vae_31838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vae_31838/02_2024/7vae_31838.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vae_31838/02_2024/7vae_31838.pdb" } 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 Residue "A ASP 24": "OD1" <-> "OD2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H ASP 109": "OD1" <-> "OD2" Residue "H TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L GLU 61": "OE1" <-> "OE2" Residue "L ASP 76": "OD1" <-> "OD2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 200": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 3.59, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.62 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: 1.50 Time building geometry restraints manager: 2.38 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: 99.03 - 106.05: 155 106.05 - 113.06: 3163 113.06 - 120.08: 1959 120.08 - 127.09: 2505 127.09 - 134.11: 68 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 2.440 nonbonded pdb=" O VAL A 203 " pdb=" OG SER A 206 " model vdw 2.223 2.440 nonbonded pdb=" O GLY H 8 " pdb=" OG1 THR H 115 " model vdw 2.237 2.440 nonbonded pdb=" NH1 ARG L 160 " pdb=" O ASN L 162 " model vdw 2.283 2.520 nonbonded pdb=" O LEU A 85 " pdb=" NH1 ARG L 33 " model vdw 2.331 2.520 ... (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 ========== 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: 0.510 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: 2.020 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.360 Find NCS groups from input model: 0.160 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.720 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 0.694 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: 0.1578 time to fit residues: 56.2762 Evaluate side-chains 238 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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: 3.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.0040 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 293 GLN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1881 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= 0.204 Angle : 0.670 8.344 7850 Z= 0.334 Chirality : 0.044 0.173 911 Planarity : 0.005 0.063 971 Dihedral : 4.339 18.739 787 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.26 % Favored : 92.60 % Rotamer: Outliers : 2.34 % Allowed : 17.03 % 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: 0.19 (0.32), residues: 730 helix: 1.27 (0.32), residues: 246 sheet: 0.44 (0.39), residues: 194 loop : -1.07 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 41 HIS 0.003 0.001 HIS H 35 PHE 0.017 0.002 PHE H 174 TYR 0.011 0.001 TYR H 183 ARG 0.005 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 259 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 244 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 36 LEU cc_start: 0.9116 (mm) cc_final: 0.8761 (mm) REVERT: A 189 LYS cc_start: 0.7692 (mmtt) cc_final: 0.7102 (tptm) REVERT: H 130 TYR cc_start: 0.8086 (m-80) cc_final: 0.7328 (m-10) REVERT: H 185 MET cc_start: 0.8981 (ppp) cc_final: 0.8680 (ppp) REVERT: L 184 LEU cc_start: 0.9035 (mt) cc_final: 0.8785 (mt) REVERT: L 200 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6441 (pm20) outliers start: 15 outliers final: 11 residues processed: 247 average time/residue: 0.1318 time to fit residues: 43.8806 Evaluate side-chains 241 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 229 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 247 ASN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain H residue 117 LEU 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 66 ASP 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: 1.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 293 GLN L 27 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: 0.7790 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5778 Z= 0.219 Angle : 0.666 9.231 7850 Z= 0.330 Chirality : 0.044 0.175 911 Planarity : 0.005 0.061 971 Dihedral : 4.418 21.803 787 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.38 % Allowed : 20.16 % 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: 1.33 (0.32), residues: 246 sheet: 0.54 (0.39), residues: 183 loop : -1.25 (0.35), residues: 301 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 0.001 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 267 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 239 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7570 (mpt-90) cc_final: 0.6709 (mtt180) REVERT: A 36 LEU cc_start: 0.9124 (mm) cc_final: 0.8774 (mm) REVERT: H 56 ASP cc_start: 0.8342 (t0) cc_final: 0.8113 (t0) REVERT: H 130 TYR cc_start: 0.7946 (m-80) cc_final: 0.7513 (m-10) REVERT: H 185 MET cc_start: 0.9105 (ppp) cc_final: 0.8718 (ppp) REVERT: L 200 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6540 (pm20) outliers start: 28 outliers final: 22 residues processed: 246 average time/residue: 0.1420 time to fit residues: 47.3205 Evaluate side-chains 237 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 300 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain H residue 117 LEU 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 66 ASP Chi-restraints excluded: chain L residue 89 LEU 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: 1.9990 chunk 49 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 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 54 HIS L 27 GLN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5778 Z= 0.258 Angle : 0.676 9.765 7850 Z= 0.335 Chirality : 0.044 0.143 911 Planarity : 0.004 0.060 971 Dihedral : 4.554 22.731 787 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 5.16 % Allowed : 23.28 % Favored : 71.56 % 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: 1.27 (0.32), residues: 245 sheet: 0.37 (0.39), residues: 183 loop : -1.30 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.018 0.002 PHE A 82 TYR 0.017 0.001 TYR L 145 ARG 0.011 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 261 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 228 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7477 (mpt-90) cc_final: 0.6645 (mtt180) REVERT: A 34 MET cc_start: 0.8038 (ttm) cc_final: 0.7781 (ttm) REVERT: A 36 LEU cc_start: 0.9056 (mm) cc_final: 0.8693 (mm) REVERT: A 138 LEU cc_start: 0.9455 (mt) cc_final: 0.9241 (mt) REVERT: H 54 TYR cc_start: 0.8326 (t80) cc_final: 0.8116 (t80) REVERT: H 56 ASP cc_start: 0.8347 (t0) cc_final: 0.8137 (t0) REVERT: H 130 TYR cc_start: 0.8036 (m-80) cc_final: 0.7513 (m-10) REVERT: H 185 MET cc_start: 0.9064 (ppp) cc_final: 0.8735 (ppp) REVERT: L 200 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6773 (pm20) outliers start: 33 outliers final: 27 residues processed: 238 average time/residue: 0.1268 time to fit residues: 41.7496 Evaluate side-chains 244 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 46 MET 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 270 LEU 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 184 THR Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 89 LEU 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 165 LEU 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: 0.0270 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.8440 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 5778 Z= 0.225 Angle : 0.684 12.148 7850 Z= 0.334 Chirality : 0.044 0.140 911 Planarity : 0.005 0.059 971 Dihedral : 4.519 23.006 787 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 5.00 % Allowed : 24.22 % Favored : 70.78 % 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: 1.27 (0.33), residues: 247 sheet: 0.37 (0.38), residues: 194 loop : -1.46 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP L 168 HIS 0.004 0.001 HIS H 35 PHE 0.018 0.001 PHE H 154 TYR 0.019 0.001 TYR L 145 ARG 0.010 0.001 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 259 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 227 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7349 (mpt-90) cc_final: 0.6611 (mtt180) REVERT: A 34 MET cc_start: 0.7995 (ttm) cc_final: 0.7755 (ttm) REVERT: A 36 LEU cc_start: 0.9064 (mm) cc_final: 0.8689 (mm) REVERT: A 138 LEU cc_start: 0.9436 (mt) cc_final: 0.9234 (mt) REVERT: H 54 TYR cc_start: 0.8332 (t80) cc_final: 0.8126 (t80) REVERT: H 179 GLN cc_start: 0.8390 (pp30) cc_final: 0.8112 (pp30) REVERT: H 185 MET cc_start: 0.9062 (ppp) cc_final: 0.8711 (ppp) REVERT: L 200 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6800 (pm20) outliers start: 32 outliers final: 27 residues processed: 237 average time/residue: 0.1244 time to fit residues: 40.5864 Evaluate side-chains 251 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 223 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 270 LEU 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 184 THR Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 66 ASP 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 200 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5778 Z= 0.217 Angle : 0.681 8.838 7850 Z= 0.334 Chirality : 0.044 0.139 911 Planarity : 0.005 0.056 971 Dihedral : 4.528 25.301 787 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 5.47 % Allowed : 25.78 % 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: -0.00 (0.32), residues: 730 helix: 1.37 (0.33), residues: 249 sheet: 0.39 (0.39), residues: 194 loop : -1.53 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP L 168 HIS 0.003 0.001 HIS A 221 PHE 0.017 0.001 PHE A 82 TYR 0.020 0.001 TYR L 145 ARG 0.008 0.001 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 273 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 238 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.8015 (p0) REVERT: A 25 ARG cc_start: 0.7331 (mpt-90) cc_final: 0.6688 (mtt180) REVERT: A 36 LEU cc_start: 0.9046 (mm) cc_final: 0.8665 (mm) REVERT: A 74 LEU cc_start: 0.8645 (tt) cc_final: 0.8388 (tt) REVERT: A 256 MET cc_start: 0.7592 (ttm) cc_final: 0.7249 (ttp) REVERT: A 283 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: H 179 GLN cc_start: 0.8455 (pp30) cc_final: 0.8184 (pp30) REVERT: H 185 MET cc_start: 0.9081 (ppp) cc_final: 0.8684 (ppp) REVERT: L 200 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6807 (pm20) outliers start: 35 outliers final: 28 residues processed: 252 average time/residue: 0.1355 time to fit residues: 46.5678 Evaluate side-chains 254 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 223 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 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 116 THR Chi-restraints excluded: chain H residue 117 LEU 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 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 66 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3503 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= 0.273 Angle : 0.723 9.025 7850 Z= 0.352 Chirality : 0.045 0.157 911 Planarity : 0.005 0.059 971 Dihedral : 4.665 26.746 787 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 6.41 % Allowed : 26.25 % Favored : 67.34 % 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 (0.31), residues: 730 helix: 1.46 (0.33), residues: 247 sheet: 0.21 (0.39), residues: 179 loop : -1.49 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.002 PHE A 82 TYR 0.022 0.001 TYR L 145 ARG 0.008 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 275 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 234 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7985 (p0) REVERT: A 25 ARG cc_start: 0.7336 (mpt-90) cc_final: 0.6709 (mtt180) REVERT: A 36 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8786 (mm) REVERT: A 74 LEU cc_start: 0.8680 (tt) cc_final: 0.8420 (tt) REVERT: A 138 LEU cc_start: 0.9551 (mt) cc_final: 0.9347 (mt) REVERT: A 189 LYS cc_start: 0.7452 (mmtt) cc_final: 0.6083 (pttt) REVERT: A 283 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: H 47 TRP cc_start: 0.8906 (t60) cc_final: 0.8340 (t60) REVERT: H 146 LEU cc_start: 0.9141 (mt) cc_final: 0.8867 (mt) REVERT: H 179 GLN cc_start: 0.8588 (pp30) cc_final: 0.8313 (pp30) REVERT: H 185 MET cc_start: 0.9105 (ppp) cc_final: 0.8694 (ppp) REVERT: L 61 GLU cc_start: 0.8607 (tp30) cc_final: 0.8162 (tm-30) REVERT: L 115 ASP cc_start: 0.7365 (m-30) cc_final: 0.7049 (m-30) REVERT: L 123 PHE cc_start: 0.7791 (m-80) cc_final: 0.7230 (m-80) REVERT: L 200 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7034 (pm20) outliers start: 41 outliers final: 31 residues processed: 251 average time/residue: 0.1321 time to fit residues: 44.9374 Evaluate side-chains 252 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 122 MET 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 51 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 184 THR Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 66 ASP 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 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: 2.9990 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 293 GLN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5778 Z= 0.251 Angle : 0.735 8.948 7850 Z= 0.353 Chirality : 0.045 0.166 911 Planarity : 0.005 0.064 971 Dihedral : 4.734 26.510 787 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % 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 : 0.00 % 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 (0.31), residues: 730 helix: 1.46 (0.33), residues: 247 sheet: -0.04 (0.39), residues: 181 loop : -1.47 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.001 PHE A 82 TYR 0.024 0.002 TYR H 50 ARG 0.007 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 fitting. rotamer outliers: 32 poor density : 233 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7947 (p0) REVERT: A 25 ARG cc_start: 0.7338 (mpt-90) cc_final: 0.6729 (mtt180) REVERT: A 36 LEU cc_start: 0.9020 (mm) cc_final: 0.8770 (mm) REVERT: A 74 LEU cc_start: 0.8681 (tt) cc_final: 0.8420 (tt) REVERT: A 93 ILE cc_start: 0.9263 (tp) cc_final: 0.9005 (tp) REVERT: A 231 PHE cc_start: 0.8628 (t80) cc_final: 0.8421 (t80) REVERT: A 283 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.8010 (m-80) REVERT: H 54 TYR cc_start: 0.8047 (t80) cc_final: 0.7784 (t80) REVERT: H 113 GLN cc_start: 0.7966 (pt0) cc_final: 0.7680 (pt0) REVERT: H 146 LEU cc_start: 0.9140 (mt) cc_final: 0.8878 (mt) REVERT: H 179 GLN cc_start: 0.8666 (pp30) cc_final: 0.8386 (pp30) REVERT: H 185 MET cc_start: 0.9081 (ppp) cc_final: 0.8708 (ppp) REVERT: L 61 GLU cc_start: 0.8620 (tp30) cc_final: 0.8169 (tm-30) REVERT: L 115 ASP cc_start: 0.7293 (m-30) cc_final: 0.7019 (m-30) REVERT: L 123 PHE cc_start: 0.7834 (m-80) cc_final: 0.7263 (m-80) REVERT: L 200 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7037 (pm20) outliers start: 32 outliers final: 29 residues processed: 245 average time/residue: 0.1332 time to fit residues: 44.7392 Evaluate side-chains 266 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 234 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 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 A residue 294 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 51 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 184 THR Chi-restraints excluded: chain H residue 202 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 66 ASP 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 165 LEU 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: 0.9980 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3807 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= 0.236 Angle : 0.741 9.850 7850 Z= 0.357 Chirality : 0.045 0.162 911 Planarity : 0.005 0.063 971 Dihedral : 4.740 26.388 787 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 5.31 % Allowed : 30.00 % Favored : 64.69 % 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: -0.10 (0.31), residues: 730 helix: 1.56 (0.33), residues: 247 sheet: 0.05 (0.38), residues: 193 loop : -1.61 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.001 PHE H 154 TYR 0.023 0.001 TYR L 145 ARG 0.008 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 271 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 237 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7914 (p0) REVERT: A 25 ARG cc_start: 0.7291 (mpt-90) cc_final: 0.6700 (mtt180) REVERT: A 36 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8753 (mm) REVERT: A 58 PRO cc_start: 0.8301 (Cg_endo) cc_final: 0.7956 (Cg_exo) REVERT: A 74 LEU cc_start: 0.8725 (tt) cc_final: 0.8447 (tt) REVERT: A 93 ILE cc_start: 0.9232 (tp) cc_final: 0.9018 (tp) REVERT: A 243 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8083 (mm) REVERT: A 283 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: H 47 TRP cc_start: 0.8859 (t60) cc_final: 0.8310 (t60) REVERT: H 54 TYR cc_start: 0.8050 (t80) cc_final: 0.7777 (t80) REVERT: H 113 GLN cc_start: 0.7954 (pt0) cc_final: 0.7670 (pt0) REVERT: H 146 LEU cc_start: 0.9131 (mt) cc_final: 0.8876 (mt) REVERT: H 179 GLN cc_start: 0.8633 (pp30) cc_final: 0.8384 (pp30) REVERT: H 185 MET cc_start: 0.9070 (ppp) cc_final: 0.8696 (ppp) REVERT: L 61 GLU cc_start: 0.8656 (tp30) cc_final: 0.8217 (tm-30) REVERT: L 115 ASP cc_start: 0.7329 (m-30) cc_final: 0.7055 (m-30) REVERT: L 123 PHE cc_start: 0.7765 (m-80) cc_final: 0.7248 (m-80) REVERT: L 200 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7037 (pm20) outliers start: 34 outliers final: 27 residues processed: 250 average time/residue: 0.1377 time to fit residues: 47.2147 Evaluate side-chains 260 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 228 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 104 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 217 VAL Chi-restraints excluded: chain A residue 243 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 116 THR Chi-restraints excluded: chain H residue 117 LEU 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 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 66 ASP 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 165 LEU 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: 3.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.0870 chunk 45 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8162 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5778 Z= 0.229 Angle : 0.771 10.479 7850 Z= 0.365 Chirality : 0.045 0.186 911 Planarity : 0.005 0.064 971 Dihedral : 4.732 26.457 787 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.84 % Allowed : 31.72 % Favored : 63.44 % 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 (0.31), residues: 730 helix: 1.50 (0.33), residues: 247 sheet: 0.03 (0.38), residues: 193 loop : -1.61 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.028 0.001 PHE A 82 TYR 0.023 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 265 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 234 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7886 (p0) REVERT: A 25 ARG cc_start: 0.7125 (mpt-90) cc_final: 0.6656 (mtt180) REVERT: A 36 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8779 (mm) REVERT: A 58 PRO cc_start: 0.8321 (Cg_endo) cc_final: 0.7984 (Cg_exo) REVERT: A 74 LEU cc_start: 0.8703 (tt) cc_final: 0.8430 (tt) REVERT: A 93 ILE cc_start: 0.9248 (tp) cc_final: 0.9015 (tp) REVERT: A 243 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8054 (mm) REVERT: A 283 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: H 47 TRP cc_start: 0.8849 (t60) cc_final: 0.8306 (t60) REVERT: H 54 TYR cc_start: 0.7997 (t80) cc_final: 0.7697 (t80) REVERT: H 113 GLN cc_start: 0.7951 (pt0) cc_final: 0.7669 (pt0) REVERT: H 146 LEU cc_start: 0.9140 (mt) cc_final: 0.8880 (mt) REVERT: H 179 GLN cc_start: 0.8633 (pp30) cc_final: 0.8397 (pp30) REVERT: H 185 MET cc_start: 0.9106 (ppp) cc_final: 0.8692 (ppp) REVERT: L 61 GLU cc_start: 0.8695 (tp30) cc_final: 0.8282 (tm-30) REVERT: L 115 ASP cc_start: 0.7362 (m-30) cc_final: 0.7048 (m-30) REVERT: L 123 PHE cc_start: 0.7747 (m-80) cc_final: 0.7227 (m-80) REVERT: L 200 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7046 (pm20) outliers start: 31 outliers final: 25 residues processed: 245 average time/residue: 0.1325 time to fit residues: 44.4850 Evaluate side-chains 260 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 230 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 104 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 217 VAL Chi-restraints excluded: chain A residue 243 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 116 THR Chi-restraints excluded: chain H residue 117 LEU 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 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 66 ASP 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 165 LEU 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: 0.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 57 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 0.0870 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN ** L 129 GLN ** 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 = 0.3893 r_free = 0.3893 target = 0.148313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121306 restraints weight = 11055.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124883 restraints weight = 5190.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127048 restraints weight = 3047.600| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3991 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= 0.204 Angle : 0.760 10.965 7850 Z= 0.358 Chirality : 0.045 0.199 911 Planarity : 0.004 0.063 971 Dihedral : 4.654 26.728 787 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.69 % Allowed : 31.25 % Favored : 64.06 % 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: -0.12 (0.31), residues: 730 helix: 1.48 (0.33), residues: 249 sheet: 0.07 (0.38), residues: 193 loop : -1.59 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 36 HIS 0.003 0.001 HIS H 35 PHE 0.025 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: 1655.87 seconds wall clock time: 30 minutes 42.42 seconds (1842.42 seconds total)