Starting phenix.real_space_refine on Thu Mar 6 09:17:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsi_32759/03_2025/7wsi_32759.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsi_32759/03_2025/7wsi_32759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsi_32759/03_2025/7wsi_32759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsi_32759/03_2025/7wsi_32759.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsi_32759/03_2025/7wsi_32759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsi_32759/03_2025/7wsi_32759.cif" } resolution = 3.32 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= 0.001 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 43 5.16 5 C 3678 2.51 5 N 913 2.21 5 O 1067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5701 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2348 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 17, 'TRANS': 288} 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: 3.53, per 1000 atoms: 0.62 Number of scatterers: 5701 At special positions: 0 Unit cell: (87.15, 72.21, 141.93, 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 43 16.00 O 1067 8.00 N 913 7.00 C 3678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 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: 1.25 Conformation dependent library (CDL) restraints added in 716.1 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 38.0% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.758A pdb=" N GLY A 19 " --> pdb=" O PRO A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 44 Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.565A pdb=" N ILE A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 70 Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 103 through 113 removed outlier: 3.888A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 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 211 removed outlier: 3.568A pdb=" N ALA A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 219 through 243 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.587A pdb=" N ARG A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) 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 309 removed outlier: 3.675A pdb=" N LYS A 309 " --> pdb=" O TRP A 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 66 removed outlier: 3.520A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY H 66 " --> pdb=" O LYS H 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 66' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.104A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 199 removed outlier: 4.367A pdb=" N SER H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.547A pdb=" N LEU L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.610A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.599A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY H 57 " --> pdb=" O ASN H 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.599A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 128 through 132 removed outlier: 4.324A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER H 187 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET H 185 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR H 184 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA H 176 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 3.791A 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 removed outlier: 3.868A pdb=" N CYS H 203 " --> pdb=" O LYS H 216 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS H 216 " --> pdb=" O CYS H 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.009A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 69 through 73 Processing sheet with id=AA8, first strand: chain 'L' and resid 122 through 123 removed outlier: 4.016A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 158 through 159 removed outlier: 6.077A pdb=" N HIS L 203 " --> pdb=" O SER L 208 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N SER L 208 " --> pdb=" O HIS L 203 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 753 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: 1.35 Time building geometry restraints manager: 1.51 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: 1736 1.35 - 1.46: 1445 1.46 - 1.58: 2593 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 5839 Sorted by residual: bond pdb=" CA GLY L 70 " pdb=" C GLY L 70 " ideal model delta sigma weight residual 1.520 1.513 0.008 7.30e-03 1.88e+04 1.06e+00 bond pdb=" N SER L 25 " pdb=" CA SER L 25 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.06e+00 bond pdb=" CA THR L 20 " pdb=" CB THR L 20 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.61e-02 3.86e+03 7.89e-01 bond pdb=" CA ALA H 16 " pdb=" CB ALA H 16 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.69e-02 3.50e+03 7.72e-01 bond pdb=" SD MET A 122 " pdb=" CE MET A 122 " ideal model delta sigma weight residual 1.791 1.770 0.021 2.50e-02 1.60e+03 7.33e-01 ... (remaining 5834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 7474 1.21 - 2.43: 343 2.43 - 3.64: 78 3.64 - 4.85: 26 4.85 - 6.07: 13 Bond angle restraints: 7934 Sorted by residual: angle pdb=" N ILE A 214 " pdb=" CA ILE A 214 " pdb=" C ILE A 214 " ideal model delta sigma weight residual 111.77 108.04 3.73 1.04e+00 9.25e-01 1.29e+01 angle pdb=" C PRO L 8 " pdb=" N SER L 9 " pdb=" CA SER L 9 " ideal model delta sigma weight residual 121.54 126.59 -5.05 1.91e+00 2.74e-01 6.98e+00 angle pdb=" CA CYS L 94 " pdb=" CB CYS L 94 " pdb=" SG CYS L 94 " ideal model delta sigma weight residual 114.40 120.23 -5.83 2.30e+00 1.89e-01 6.43e+00 angle pdb=" C ASP A 149 " pdb=" N LEU A 150 " pdb=" CA LEU A 150 " ideal model delta sigma weight residual 121.54 126.15 -4.61 1.91e+00 2.74e-01 5.82e+00 angle pdb=" N THR L 169 " pdb=" CA THR L 169 " pdb=" C THR L 169 " ideal model delta sigma weight residual 110.53 107.76 2.77 1.29e+00 6.01e-01 4.61e+00 ... (remaining 7929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.97: 3061 13.97 - 27.94: 325 27.94 - 41.91: 84 41.91 - 55.87: 12 55.87 - 69.84: 2 Dihedral angle restraints: 3484 sinusoidal: 1332 harmonic: 2152 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 93.00 158.44 -65.44 1 1.00e+01 1.00e-02 5.61e+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 -86.00 -118.30 32.30 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" CA TYR L 92 " pdb=" C TYR L 92 " pdb=" N TYR L 93 " pdb=" CA TYR L 93 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 559 0.032 - 0.064: 241 0.064 - 0.096: 77 0.096 - 0.127: 37 0.127 - 0.159: 4 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA ILE L 54 " pdb=" N ILE L 54 " pdb=" C ILE L 54 " pdb=" CB ILE L 54 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-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 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE A 145 " pdb=" N ILE A 145 " pdb=" C ILE A 145 " pdb=" CB ILE A 145 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 915 not shown) Planarity restraints: 981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 64 " 0.041 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO L 65 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 65 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 65 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 180 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 181 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 49 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO L 50 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO L 50 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 50 " -0.020 5.00e-02 4.00e+02 ... (remaining 978 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 82 2.68 - 3.23: 5605 3.23 - 3.79: 8449 3.79 - 4.34: 11132 4.34 - 4.90: 18947 Nonbonded interactions: 44215 Sorted by model distance: nonbonded pdb=" OD1 ASP H 102 " pdb=" N GLY H 103 " model vdw 2.122 3.120 nonbonded pdb=" OG SER A 105 " pdb=" OE1 GLU A 257 " model vdw 2.229 3.040 nonbonded pdb=" NE2 GLN L 96 " pdb=" OG1 THR L 102 " model vdw 2.328 3.120 nonbonded pdb=" NH1 ARG L 160 " pdb=" O ASN L 162 " model vdw 2.340 3.120 nonbonded pdb=" O TYR L 55 " pdb=" OG1 THR L 59 " model vdw 2.354 3.040 ... (remaining 44210 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.440 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 0.027 5839 Z= 0.199 Angle : 0.668 6.068 7934 Z= 0.349 Chirality : 0.043 0.159 918 Planarity : 0.005 0.063 981 Dihedral : 12.247 69.843 2099 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -0.23 (0.32), residues: 737 helix: 0.97 (0.34), residues: 241 sheet: 0.43 (0.39), residues: 195 loop : -1.50 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 41 HIS 0.002 0.001 HIS H 106 PHE 0.018 0.001 PHE A 292 TYR 0.017 0.002 TYR A 69 ARG 0.004 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TRP cc_start: 0.5403 (m-10) cc_final: 0.5077 (m-10) REVERT: H 3 GLN cc_start: 0.7813 (pp30) cc_final: 0.7395 (pp30) REVERT: H 117 LEU cc_start: 0.8462 (tt) cc_final: 0.8099 (tp) REVERT: L 42 TYR cc_start: 0.8120 (m-80) cc_final: 0.7786 (m-80) REVERT: L 44 GLN cc_start: 0.8043 (tt0) cc_final: 0.7616 (tt0) REVERT: L 128 GLU cc_start: 0.7847 (pm20) cc_final: 0.7550 (pm20) REVERT: L 143 ASN cc_start: 0.8175 (m-40) cc_final: 0.7957 (m-40) REVERT: L 160 ARG cc_start: 0.8007 (ptm-80) cc_final: 0.7635 (ptp90) REVERT: L 168 TRP cc_start: 0.8956 (m-90) cc_final: 0.8650 (m-90) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1663 time to fit residues: 63.8106 Evaluate side-chains 234 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN H 39 GLN L 6 GLN L 215 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.142690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113668 restraints weight = 10613.189| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.60 r_work: 0.3250 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5839 Z= 0.242 Angle : 0.735 7.887 7934 Z= 0.368 Chirality : 0.045 0.153 918 Planarity : 0.005 0.075 981 Dihedral : 4.631 16.656 794 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.06 % Favored : 92.81 % Rotamer: Outliers : 4.33 % Allowed : 16.54 % Favored : 79.13 % 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: -0.44 (0.31), residues: 737 helix: 0.86 (0.33), residues: 253 sheet: 0.44 (0.40), residues: 182 loop : -1.79 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.002 0.001 HIS L 203 PHE 0.017 0.001 PHE A 292 TYR 0.020 0.002 TYR L 98 ARG 0.005 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8723 (t80) cc_final: 0.8430 (t80) REVERT: A 176 LEU cc_start: 0.8414 (tt) cc_final: 0.7706 (tt) REVERT: A 180 ARG cc_start: 0.7831 (tmt170) cc_final: 0.7292 (ttp80) REVERT: A 246 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7585 (mm) REVERT: A 256 MET cc_start: 0.8057 (ttm) cc_final: 0.7782 (ttm) REVERT: H 3 GLN cc_start: 0.8934 (pp30) cc_final: 0.7958 (pp30) REVERT: H 130 TYR cc_start: 0.9052 (m-10) cc_final: 0.8330 (m-80) REVERT: L 27 GLN cc_start: 0.8434 (pm20) cc_final: 0.8144 (pm20) REVERT: L 29 LEU cc_start: 0.9587 (pp) cc_final: 0.9357 (pp) REVERT: L 48 GLN cc_start: 0.8037 (mp10) cc_final: 0.7834 (mp10) REVERT: L 85 GLN cc_start: 0.6995 (tm-30) cc_final: 0.6787 (tm-30) REVERT: L 87 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8557 (pp20) REVERT: L 160 ARG cc_start: 0.8328 (ptm-80) cc_final: 0.7936 (ptp90) REVERT: L 198 THR cc_start: 0.8839 (m) cc_final: 0.8602 (p) REVERT: L 200 GLU cc_start: 0.7310 (tt0) cc_final: 0.7085 (tt0) outliers start: 28 outliers final: 17 residues processed: 237 average time/residue: 0.1420 time to fit residues: 45.2096 Evaluate side-chains 234 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 136 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN L 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106033 restraints weight = 10782.287| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.62 r_work: 0.3136 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5839 Z= 0.391 Angle : 0.755 7.976 7934 Z= 0.379 Chirality : 0.047 0.147 918 Planarity : 0.005 0.045 981 Dihedral : 4.888 18.559 794 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 7.11 % Allowed : 20.56 % Favored : 72.33 % 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: -0.63 (0.31), residues: 737 helix: 0.72 (0.33), residues: 255 sheet: 0.39 (0.41), residues: 166 loop : -1.87 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 305 HIS 0.004 0.001 HIS H 35 PHE 0.023 0.002 PHE H 154 TYR 0.028 0.002 TYR H 183 ARG 0.005 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7231 (t80) REVERT: A 50 LYS cc_start: 0.8686 (mmmt) cc_final: 0.8265 (mttp) REVERT: A 112 MET cc_start: 0.8754 (mmp) cc_final: 0.8549 (mmp) REVERT: A 133 MET cc_start: 0.8770 (ppp) cc_final: 0.8555 (ppp) REVERT: A 143 ARG cc_start: 0.8577 (ttt180) cc_final: 0.7674 (mmt90) REVERT: A 223 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8248 (mt) REVERT: H 3 GLN cc_start: 0.9034 (pp30) cc_final: 0.8016 (pp30) REVERT: H 98 ARG cc_start: 0.8809 (tmm-80) cc_final: 0.8509 (tmm-80) REVERT: H 130 TYR cc_start: 0.9056 (m-10) cc_final: 0.8338 (m-80) REVERT: L 27 GLN cc_start: 0.8659 (pm20) cc_final: 0.8320 (pm20) REVERT: L 35 ARG cc_start: 0.8823 (mmt90) cc_final: 0.8541 (mmt90) REVERT: L 48 GLN cc_start: 0.8262 (mp10) cc_final: 0.7580 (mp10) REVERT: L 85 GLN cc_start: 0.7192 (tm-30) cc_final: 0.6951 (tm-30) REVERT: L 87 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8666 (pp20) REVERT: L 123 PHE cc_start: 0.9296 (m-80) cc_final: 0.8984 (m-80) REVERT: L 161 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8689 (tm-30) REVERT: L 180 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7201 (tpt) outliers start: 46 outliers final: 33 residues processed: 236 average time/residue: 0.1568 time to fit residues: 48.5561 Evaluate side-chains 247 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 15 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 67 optimal weight: 0.0060 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110158 restraints weight = 10793.708| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.67 r_work: 0.3199 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5839 Z= 0.183 Angle : 0.684 8.767 7934 Z= 0.337 Chirality : 0.045 0.153 918 Planarity : 0.004 0.045 981 Dihedral : 4.564 17.625 794 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 5.10 % Allowed : 23.96 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.32), residues: 737 helix: 0.86 (0.34), residues: 260 sheet: 0.60 (0.42), residues: 166 loop : -1.83 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.019 0.001 PHE A 292 TYR 0.021 0.002 TYR H 183 ARG 0.003 0.000 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8090 (m-30) cc_final: 0.7874 (m-30) REVERT: A 50 LYS cc_start: 0.8472 (mmmt) cc_final: 0.7995 (mttp) REVERT: A 143 ARG cc_start: 0.8425 (ttt180) cc_final: 0.7501 (mmt90) REVERT: A 167 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8260 (tt) REVERT: A 176 LEU cc_start: 0.8675 (tt) cc_final: 0.8317 (tt) REVERT: A 223 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8183 (mt) REVERT: A 246 LEU cc_start: 0.8139 (mt) cc_final: 0.7894 (mm) REVERT: H 3 GLN cc_start: 0.9018 (pp30) cc_final: 0.7987 (pp30) REVERT: H 130 TYR cc_start: 0.9031 (m-10) cc_final: 0.8247 (m-80) REVERT: L 27 GLN cc_start: 0.8543 (pm20) cc_final: 0.8045 (pm20) REVERT: L 29 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9211 (pp) REVERT: L 48 GLN cc_start: 0.8239 (mp10) cc_final: 0.7541 (mp10) REVERT: L 87 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8619 (pp20) REVERT: L 123 PHE cc_start: 0.9273 (m-80) cc_final: 0.8873 (m-80) REVERT: L 161 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8543 (tm-30) REVERT: L 168 TRP cc_start: 0.9459 (m-90) cc_final: 0.8930 (m-90) REVERT: L 180 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7504 (tpt) outliers start: 33 outliers final: 20 residues processed: 237 average time/residue: 0.1494 time to fit residues: 47.7224 Evaluate side-chains 245 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 211 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.0030 chunk 60 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109455 restraints weight = 10644.662| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.69 r_work: 0.3196 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5839 Z= 0.205 Angle : 0.692 12.101 7934 Z= 0.337 Chirality : 0.044 0.160 918 Planarity : 0.004 0.035 981 Dihedral : 4.522 18.067 794 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.26 % Allowed : 24.88 % Favored : 69.86 % 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: -0.36 (0.32), residues: 737 helix: 0.85 (0.33), residues: 261 sheet: 0.69 (0.42), residues: 166 loop : -1.77 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.001 PHE A 292 TYR 0.023 0.002 TYR H 183 ARG 0.003 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8847 (t80) cc_final: 0.8620 (t80) REVERT: A 24 ASP cc_start: 0.8151 (m-30) cc_final: 0.7905 (m-30) REVERT: A 46 MET cc_start: 0.9033 (mtt) cc_final: 0.8742 (mtp) REVERT: A 50 LYS cc_start: 0.8567 (mmmt) cc_final: 0.8103 (mttp) REVERT: A 133 MET cc_start: 0.8692 (ppp) cc_final: 0.8462 (ppp) REVERT: A 223 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8162 (mt) REVERT: H 3 GLN cc_start: 0.9031 (pp30) cc_final: 0.7998 (pp30) REVERT: H 81 MET cc_start: 0.9173 (ttm) cc_final: 0.8963 (ttt) REVERT: H 90 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8766 (m-30) REVERT: H 98 ARG cc_start: 0.8795 (tmm-80) cc_final: 0.8498 (tmm-80) REVERT: H 117 LEU cc_start: 0.9386 (tp) cc_final: 0.9185 (tt) REVERT: H 130 TYR cc_start: 0.8897 (m-10) cc_final: 0.8418 (m-80) REVERT: L 27 GLN cc_start: 0.8596 (pm20) cc_final: 0.8116 (pm20) REVERT: L 29 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9209 (pp) REVERT: L 48 GLN cc_start: 0.8235 (mp10) cc_final: 0.7578 (mp10) REVERT: L 87 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8580 (pp20) REVERT: L 123 PHE cc_start: 0.9177 (m-80) cc_final: 0.8934 (m-80) REVERT: L 161 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8470 (tm-30) REVERT: L 168 TRP cc_start: 0.9452 (m-90) cc_final: 0.8893 (m-90) REVERT: L 180 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7471 (tpt) outliers start: 34 outliers final: 20 residues processed: 226 average time/residue: 0.1346 time to fit residues: 41.3557 Evaluate side-chains 230 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 12 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN H 39 GLN L 6 GLN L 44 GLN L 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.138674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108907 restraints weight = 10687.981| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.69 r_work: 0.3190 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5839 Z= 0.222 Angle : 0.685 9.345 7934 Z= 0.335 Chirality : 0.044 0.177 918 Planarity : 0.004 0.037 981 Dihedral : 4.492 16.502 794 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 6.03 % Allowed : 24.88 % Favored : 69.09 % 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: -0.24 (0.32), residues: 737 helix: 1.05 (0.34), residues: 255 sheet: 0.80 (0.43), residues: 165 loop : -1.77 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.001 PHE A 292 TYR 0.024 0.002 TYR H 183 ARG 0.004 0.000 ARG L 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8901 (t80) cc_final: 0.8697 (t80) REVERT: A 24 ASP cc_start: 0.8132 (m-30) cc_final: 0.7893 (m-30) REVERT: A 50 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8104 (mttp) REVERT: A 112 MET cc_start: 0.8570 (mmp) cc_final: 0.8313 (mmt) REVERT: A 141 TYR cc_start: 0.9004 (m-80) cc_final: 0.8261 (m-80) REVERT: A 223 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8068 (mt) REVERT: H 3 GLN cc_start: 0.9057 (pp30) cc_final: 0.8013 (pp30) REVERT: H 90 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8842 (m-30) REVERT: H 117 LEU cc_start: 0.9418 (tp) cc_final: 0.9213 (tt) REVERT: H 130 TYR cc_start: 0.8900 (m-10) cc_final: 0.8392 (m-80) REVERT: H 215 ASP cc_start: 0.8683 (t70) cc_final: 0.7985 (p0) REVERT: L 27 GLN cc_start: 0.8611 (pm20) cc_final: 0.8129 (pm20) REVERT: L 29 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9211 (pp) REVERT: L 48 GLN cc_start: 0.8249 (mp10) cc_final: 0.7603 (mp10) REVERT: L 85 GLN cc_start: 0.7334 (tm-30) cc_final: 0.6597 (tm-30) REVERT: L 161 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8416 (tm-30) REVERT: L 168 TRP cc_start: 0.9466 (m-90) cc_final: 0.8874 (m-90) REVERT: L 180 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7471 (tpt) outliers start: 39 outliers final: 26 residues processed: 220 average time/residue: 0.1305 time to fit residues: 39.3612 Evaluate side-chains 233 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 12 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 59 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.0020 chunk 63 optimal weight: 2.9990 overall best weight: 0.8490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN L 6 GLN L 44 GLN L 215 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.138395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108937 restraints weight = 10684.871| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.67 r_work: 0.3190 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5839 Z= 0.222 Angle : 0.681 9.656 7934 Z= 0.334 Chirality : 0.044 0.175 918 Planarity : 0.004 0.035 981 Dihedral : 4.474 16.576 794 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 5.41 % Allowed : 26.28 % Favored : 68.32 % 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: -0.21 (0.32), residues: 737 helix: 1.12 (0.34), residues: 254 sheet: 0.80 (0.43), residues: 165 loop : -1.76 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.001 PHE A 292 TYR 0.023 0.002 TYR H 183 ARG 0.004 0.000 ARG L 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8109 (m-30) cc_final: 0.7877 (m-30) REVERT: A 46 MET cc_start: 0.9037 (mtt) cc_final: 0.8736 (mtp) REVERT: A 50 LYS cc_start: 0.8583 (mmmt) cc_final: 0.8126 (mttp) REVERT: A 141 TYR cc_start: 0.9000 (m-80) cc_final: 0.8215 (m-80) REVERT: A 183 TYR cc_start: 0.6119 (OUTLIER) cc_final: 0.5556 (m-10) REVERT: A 223 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8064 (mt) REVERT: A 277 GLU cc_start: 0.8666 (mp0) cc_final: 0.8456 (mp0) REVERT: H 3 GLN cc_start: 0.9038 (pp30) cc_final: 0.8003 (pp30) REVERT: H 90 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8847 (m-30) REVERT: H 98 ARG cc_start: 0.8868 (tmm-80) cc_final: 0.8520 (tmm-80) REVERT: H 117 LEU cc_start: 0.9423 (tp) cc_final: 0.9206 (tt) REVERT: H 130 TYR cc_start: 0.8895 (m-10) cc_final: 0.8397 (m-80) REVERT: H 215 ASP cc_start: 0.8591 (t70) cc_final: 0.7934 (p0) REVERT: L 27 GLN cc_start: 0.8627 (pm20) cc_final: 0.8143 (pm20) REVERT: L 29 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9216 (pp) REVERT: L 35 ARG cc_start: 0.8705 (mmt90) cc_final: 0.8471 (mmt90) REVERT: L 48 GLN cc_start: 0.8291 (mp10) cc_final: 0.7664 (mp10) REVERT: L 85 GLN cc_start: 0.7374 (tm-30) cc_final: 0.7125 (tm-30) REVERT: L 87 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8712 (pp20) REVERT: L 110 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8251 (mp0) REVERT: L 161 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8332 (tm-30) REVERT: L 168 TRP cc_start: 0.9427 (m-90) cc_final: 0.8838 (m-90) REVERT: L 180 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7593 (tpt) outliers start: 35 outliers final: 22 residues processed: 223 average time/residue: 0.1367 time to fit residues: 41.3148 Evaluate side-chains 253 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 59 optimal weight: 0.0040 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 65 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN L 6 GLN L 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.139516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110395 restraints weight = 10601.985| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.65 r_work: 0.3235 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5839 Z= 0.199 Angle : 0.679 9.870 7934 Z= 0.330 Chirality : 0.044 0.181 918 Planarity : 0.004 0.035 981 Dihedral : 4.403 16.205 794 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 5.10 % Allowed : 27.05 % Favored : 67.85 % 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: 737 helix: 1.19 (0.34), residues: 254 sheet: 0.86 (0.44), residues: 165 loop : -1.77 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.001 PHE A 292 TYR 0.022 0.002 TYR H 183 ARG 0.004 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7970 (m-30) cc_final: 0.7754 (m-30) REVERT: A 50 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8120 (mttp) REVERT: A 141 TYR cc_start: 0.8995 (m-80) cc_final: 0.8241 (m-80) REVERT: A 167 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8202 (tt) REVERT: A 176 LEU cc_start: 0.8768 (tt) cc_final: 0.8403 (tt) REVERT: A 223 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.8003 (mt) REVERT: A 277 GLU cc_start: 0.8731 (mp0) cc_final: 0.8477 (mp0) REVERT: H 3 GLN cc_start: 0.9004 (pp30) cc_final: 0.7963 (pp30) REVERT: H 90 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8821 (m-30) REVERT: H 98 ARG cc_start: 0.8866 (tmm-80) cc_final: 0.8516 (tmm-80) REVERT: H 100 TYR cc_start: 0.8929 (t80) cc_final: 0.8478 (t80) REVERT: H 130 TYR cc_start: 0.8674 (m-10) cc_final: 0.8442 (m-80) REVERT: H 189 VAL cc_start: 0.9032 (p) cc_final: 0.8823 (m) REVERT: H 215 ASP cc_start: 0.8533 (t70) cc_final: 0.7965 (p0) REVERT: L 29 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9206 (pp) REVERT: L 44 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.8727 (tt0) REVERT: L 48 GLN cc_start: 0.8317 (mp10) cc_final: 0.7692 (mp10) REVERT: L 85 GLN cc_start: 0.7325 (tm-30) cc_final: 0.7093 (tm-30) REVERT: L 87 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8738 (pp20) REVERT: L 110 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8267 (mp0) REVERT: L 161 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8261 (tm-30) REVERT: L 168 TRP cc_start: 0.9442 (m-90) cc_final: 0.8864 (m-90) REVERT: L 180 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7598 (tpt) outliers start: 33 outliers final: 21 residues processed: 233 average time/residue: 0.1431 time to fit residues: 45.2528 Evaluate side-chains 233 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 9 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.141427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112267 restraints weight = 10681.867| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.66 r_work: 0.3252 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5839 Z= 0.199 Angle : 0.711 9.961 7934 Z= 0.340 Chirality : 0.044 0.200 918 Planarity : 0.004 0.034 981 Dihedral : 4.366 15.717 794 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.33 % Allowed : 28.44 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.32), residues: 737 helix: 1.12 (0.34), residues: 258 sheet: 0.80 (0.43), residues: 173 loop : -1.74 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.001 PHE A 292 TYR 0.021 0.001 TYR H 183 ARG 0.003 0.000 ARG L 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7943 (m-30) cc_final: 0.7730 (m-30) REVERT: A 46 MET cc_start: 0.9069 (mtt) cc_final: 0.8737 (mtp) REVERT: A 50 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8126 (mttp) REVERT: A 106 ASN cc_start: 0.8675 (m110) cc_final: 0.8038 (m-40) REVERT: A 141 TYR cc_start: 0.9001 (m-80) cc_final: 0.8289 (m-80) REVERT: A 223 ILE cc_start: 0.8231 (mt) cc_final: 0.7994 (mt) REVERT: A 277 GLU cc_start: 0.8690 (mp0) cc_final: 0.8445 (mp0) REVERT: H 3 GLN cc_start: 0.8989 (pp30) cc_final: 0.7957 (pp30) REVERT: H 130 TYR cc_start: 0.8793 (m-10) cc_final: 0.8393 (m-80) REVERT: H 189 VAL cc_start: 0.9053 (p) cc_final: 0.8844 (m) REVERT: H 215 ASP cc_start: 0.8391 (t70) cc_final: 0.7868 (p0) REVERT: L 29 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9234 (pp) REVERT: L 44 GLN cc_start: 0.9396 (OUTLIER) cc_final: 0.8755 (tt0) REVERT: L 48 GLN cc_start: 0.8287 (mp10) cc_final: 0.7673 (mp10) REVERT: L 85 GLN cc_start: 0.7360 (tm-30) cc_final: 0.7125 (tm-30) REVERT: L 87 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8728 (pp20) REVERT: L 110 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8235 (mp0) REVERT: L 161 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8209 (tm-30) REVERT: L 168 TRP cc_start: 0.9442 (m-90) cc_final: 0.8933 (m-90) REVERT: L 180 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7609 (tpt) outliers start: 28 outliers final: 20 residues processed: 232 average time/residue: 0.1474 time to fit residues: 46.2125 Evaluate side-chains 230 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 20 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 13 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN L 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.140024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110116 restraints weight = 10838.125| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.72 r_work: 0.3211 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 5839 Z= 0.218 Angle : 0.728 9.913 7934 Z= 0.346 Chirality : 0.044 0.196 918 Planarity : 0.004 0.034 981 Dihedral : 4.389 16.085 794 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.71 % Allowed : 29.21 % Favored : 67.08 % 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: -0.08 (0.33), residues: 737 helix: 1.20 (0.34), residues: 258 sheet: 0.80 (0.43), residues: 173 loop : -1.73 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.002 0.001 HIS H 35 PHE 0.022 0.001 PHE A 292 TYR 0.022 0.002 TYR H 183 ARG 0.003 0.000 ARG L 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.9021 (mtt) cc_final: 0.8700 (mtp) REVERT: A 50 LYS cc_start: 0.8581 (mmmt) cc_final: 0.8166 (mttp) REVERT: A 106 ASN cc_start: 0.8762 (m110) cc_final: 0.8104 (m-40) REVERT: A 141 TYR cc_start: 0.8989 (m-80) cc_final: 0.8352 (m-80) REVERT: A 223 ILE cc_start: 0.8216 (mt) cc_final: 0.7966 (mt) REVERT: A 277 GLU cc_start: 0.8684 (mp0) cc_final: 0.8443 (mp0) REVERT: H 3 GLN cc_start: 0.9030 (pp30) cc_final: 0.8063 (pp30) REVERT: H 100 TYR cc_start: 0.8909 (t80) cc_final: 0.8373 (t80) REVERT: H 117 LEU cc_start: 0.9391 (tp) cc_final: 0.9150 (tt) REVERT: H 130 TYR cc_start: 0.8730 (m-10) cc_final: 0.8466 (m-80) REVERT: H 189 VAL cc_start: 0.9072 (p) cc_final: 0.8848 (m) REVERT: L 29 LEU cc_start: 0.9665 (OUTLIER) cc_final: 0.9227 (pp) REVERT: L 44 GLN cc_start: 0.9392 (OUTLIER) cc_final: 0.8748 (tt0) REVERT: L 48 GLN cc_start: 0.8328 (mp10) cc_final: 0.7710 (mp10) REVERT: L 85 GLN cc_start: 0.7439 (tm-30) cc_final: 0.7191 (tm-30) REVERT: L 87 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8706 (pp20) REVERT: L 160 ARG cc_start: 0.8221 (ptm-80) cc_final: 0.6953 (ptm160) REVERT: L 161 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8110 (tm-30) REVERT: L 168 TRP cc_start: 0.9456 (m-90) cc_final: 0.8931 (m-90) REVERT: L 180 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7591 (tpt) outliers start: 24 outliers final: 18 residues processed: 217 average time/residue: 0.1421 time to fit residues: 42.0412 Evaluate side-chains 229 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 21 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110865 restraints weight = 10771.024| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.72 r_work: 0.3224 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5839 Z= 0.204 Angle : 0.724 10.279 7934 Z= 0.344 Chirality : 0.045 0.204 918 Planarity : 0.004 0.034 981 Dihedral : 4.411 15.737 794 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.71 % Allowed : 29.21 % Favored : 67.08 % 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 (0.33), residues: 737 helix: 1.41 (0.35), residues: 251 sheet: 0.77 (0.43), residues: 174 loop : -1.62 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.022 0.001 PHE A 292 TYR 0.021 0.001 TYR H 183 ARG 0.003 0.000 ARG L 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3036.59 seconds wall clock time: 53 minutes 26.80 seconds (3206.80 seconds total)