Starting phenix.real_space_refine on Thu Jun 5 07:57:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsi_32759/06_2025/7wsi_32759.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsi_32759/06_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_32759/06_2025/7wsi_32759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsi_32759/06_2025/7wsi_32759.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsi_32759/06_2025/7wsi_32759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsi_32759/06_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-5710/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: 3.94, per 1000 atoms: 0.69 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: 1.24 Conformation dependent library (CDL) restraints added in 736.6 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: 1.55 Time building geometry restraints manager: 1.52 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 17.440 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.210 ------------------------------------------------------------------------------- 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 5842 Z= 0.142 Angle : 0.668 6.068 7940 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 Details of bonding type rmsd hydrogen bonds : bond 0.17774 ( 271) hydrogen bonds : angle 6.60305 ( 753) SS BOND : bond 0.00348 ( 3) SS BOND : angle 0.81728 ( 6) covalent geometry : bond 0.00302 ( 5839) covalent geometry : angle 0.66803 ( 7934) *********************** 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 : 0.578 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: 0.1652 time to fit residues: 63.5447 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 : 0.725 ------------------------------------------------------------------------------- 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: 0.5980 chunk 55 optimal weight: 0.9980 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: 1.9990 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN H 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 = 0.3802 r_free = 0.3802 target = 0.142904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113858 restraints weight = 10584.965| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.64 r_work: 0.3256 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5842 Z= 0.149 Angle : 0.733 7.997 7940 Z= 0.366 Chirality : 0.045 0.155 918 Planarity : 0.005 0.079 981 Dihedral : 4.642 16.522 794 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.19 % Favored : 92.67 % Rotamer: Outliers : 4.64 % Allowed : 16.23 % 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: -0.42 (0.31), residues: 737 helix: 0.87 (0.34), residues: 252 sheet: 0.44 (0.40), residues: 182 loop : -1.75 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 153 HIS 0.002 0.001 HIS L 203 PHE 0.015 0.001 PHE A 292 TYR 0.021 0.002 TYR L 98 ARG 0.006 0.001 ARG L 60 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 271) hydrogen bonds : angle 5.10861 ( 753) SS BOND : bond 0.00206 ( 3) SS BOND : angle 0.94177 ( 6) covalent geometry : bond 0.00341 ( 5839) covalent geometry : angle 0.73300 ( 7934) *********************** 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 259 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8728 (t80) cc_final: 0.8445 (t80) REVERT: A 176 LEU cc_start: 0.8396 (tt) cc_final: 0.7701 (tt) REVERT: A 180 ARG cc_start: 0.7815 (tmt170) cc_final: 0.7296 (ttp80) REVERT: A 246 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7631 (mm) REVERT: A 256 MET cc_start: 0.8047 (ttm) cc_final: 0.7767 (ttm) REVERT: H 3 GLN cc_start: 0.8939 (pp30) cc_final: 0.7971 (pp30) REVERT: H 130 TYR cc_start: 0.9039 (m-10) cc_final: 0.8326 (m-80) REVERT: L 4 MET cc_start: 0.9208 (mmm) cc_final: 0.8994 (mmm) REVERT: L 27 GLN cc_start: 0.8428 (pm20) cc_final: 0.8142 (pm20) REVERT: L 29 LEU cc_start: 0.9578 (pp) cc_final: 0.9326 (pp) REVERT: L 87 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8485 (pp20) REVERT: L 160 ARG cc_start: 0.8307 (ptm-80) cc_final: 0.7927 (ptp90) REVERT: L 198 THR cc_start: 0.8742 (m) cc_final: 0.8481 (p) REVERT: L 200 GLU cc_start: 0.7326 (tt0) cc_final: 0.7113 (tt0) outliers start: 30 outliers final: 19 residues processed: 238 average time/residue: 0.1397 time to fit residues: 44.9564 Evaluate side-chains 234 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 161 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 215 MET 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: 2.9990 chunk 55 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 247 ASN L 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.135361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105622 restraints weight = 10779.510| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.64 r_work: 0.3149 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 5842 Z= 0.237 Angle : 0.742 8.065 7940 Z= 0.372 Chirality : 0.046 0.149 918 Planarity : 0.005 0.044 981 Dihedral : 4.838 18.433 794 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 6.34 % Allowed : 20.56 % Favored : 73.11 % 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: -0.56 (0.31), residues: 737 helix: 0.77 (0.33), residues: 255 sheet: 0.46 (0.41), residues: 166 loop : -1.82 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 305 HIS 0.003 0.001 HIS H 35 PHE 0.021 0.002 PHE H 154 TYR 0.027 0.002 TYR H 183 ARG 0.005 0.001 ARG L 60 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 271) hydrogen bonds : angle 4.81755 ( 753) SS BOND : bond 0.00409 ( 3) SS BOND : angle 0.74298 ( 6) covalent geometry : bond 0.00552 ( 5839) covalent geometry : angle 0.74173 ( 7934) *********************** 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 259 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8241 (mttp) REVERT: A 133 MET cc_start: 0.8768 (ppp) cc_final: 0.8566 (ppp) REVERT: A 143 ARG cc_start: 0.8576 (ttt180) cc_final: 0.7626 (mmt90) REVERT: A 223 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8208 (mt) REVERT: H 3 GLN cc_start: 0.9024 (pp30) cc_final: 0.8004 (pp30) REVERT: H 48 ILE cc_start: 0.9365 (mt) cc_final: 0.9095 (mm) REVERT: H 130 TYR cc_start: 0.9070 (m-10) cc_final: 0.8303 (m-80) REVERT: L 27 GLN cc_start: 0.8648 (pm20) cc_final: 0.8318 (pm20) REVERT: L 35 ARG cc_start: 0.8836 (mmt90) cc_final: 0.8571 (mmt90) REVERT: L 85 GLN cc_start: 0.7384 (tm-30) cc_final: 0.7159 (tm-30) REVERT: L 87 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8628 (pp20) REVERT: L 123 PHE cc_start: 0.9292 (m-80) cc_final: 0.9049 (m-80) REVERT: L 161 GLN cc_start: 0.8961 (tm-30) cc_final: 0.8663 (tm-30) REVERT: L 180 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7226 (tpt) outliers start: 41 outliers final: 29 residues processed: 233 average time/residue: 0.1603 time to fit residues: 49.0975 Evaluate side-chains 243 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 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 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 159 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 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 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 102 THR 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: 0.9980 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.109694 restraints weight = 10883.155| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.71 r_work: 0.3197 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5842 Z= 0.136 Angle : 0.691 8.458 7940 Z= 0.339 Chirality : 0.045 0.151 918 Planarity : 0.004 0.043 981 Dihedral : 4.615 17.943 794 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 5.56 % Allowed : 23.34 % Favored : 71.10 % 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 (0.31), residues: 737 helix: 0.81 (0.33), residues: 260 sheet: 0.60 (0.42), residues: 166 loop : -1.77 (0.34), 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 0.018 0.001 PHE A 292 TYR 0.021 0.002 TYR H 183 ARG 0.003 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 271) hydrogen bonds : angle 4.63431 ( 753) SS BOND : bond 0.00255 ( 3) SS BOND : angle 0.65095 ( 6) covalent geometry : bond 0.00313 ( 5839) covalent geometry : angle 0.69108 ( 7934) *********************** 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 270 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8703 (t80) cc_final: 0.8500 (t80) REVERT: A 24 ASP cc_start: 0.8136 (m-30) cc_final: 0.7902 (m-30) REVERT: A 50 LYS cc_start: 0.8555 (mmmt) cc_final: 0.8116 (mttp) REVERT: A 133 MET cc_start: 0.8772 (ppp) cc_final: 0.8515 (ppp) REVERT: A 143 ARG cc_start: 0.8482 (ttt180) cc_final: 0.7512 (mmt90) REVERT: A 167 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8263 (tt) REVERT: A 176 LEU cc_start: 0.8677 (tt) cc_final: 0.8344 (tt) REVERT: A 223 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8196 (mt) REVERT: A 246 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7923 (mm) REVERT: H 3 GLN cc_start: 0.9026 (pp30) cc_final: 0.7994 (pp30) REVERT: H 130 TYR cc_start: 0.8871 (m-80) cc_final: 0.8289 (m-80) REVERT: L 27 GLN cc_start: 0.8567 (pm20) cc_final: 0.8078 (pm20) REVERT: L 29 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9206 (pp) REVERT: L 87 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8600 (pp20) REVERT: L 110 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8223 (mp0) REVERT: L 161 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8500 (tm-30) REVERT: L 168 TRP cc_start: 0.9475 (m-90) cc_final: 0.8922 (m-90) REVERT: L 180 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7432 (tpt) outliers start: 36 outliers final: 22 residues processed: 242 average time/residue: 0.1730 time to fit residues: 55.9882 Evaluate side-chains 243 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 51 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU 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 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 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 87 GLU Chi-restraints excluded: chain L residue 102 THR 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 181 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.0370 chunk 60 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN L 6 GLN L 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.109660 restraints weight = 10697.331| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.67 r_work: 0.3200 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5842 Z= 0.140 Angle : 0.693 9.248 7940 Z= 0.337 Chirality : 0.045 0.162 918 Planarity : 0.004 0.035 981 Dihedral : 4.539 16.890 794 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 6.34 % Allowed : 24.42 % Favored : 69.24 % 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: 0.90 (0.34), residues: 260 sheet: 0.58 (0.42), residues: 166 loop : -1.72 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.001 PHE A 292 TYR 0.024 0.002 TYR H 183 ARG 0.003 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03265 ( 271) hydrogen bonds : angle 4.56799 ( 753) SS BOND : bond 0.00318 ( 3) SS BOND : angle 0.64200 ( 6) covalent geometry : bond 0.00325 ( 5839) covalent geometry : angle 0.69266 ( 7934) *********************** 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 256 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8142 (m-30) cc_final: 0.7905 (m-30) REVERT: A 50 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8107 (mttp) REVERT: A 223 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8173 (mt) REVERT: H 3 GLN cc_start: 0.9046 (pp30) cc_final: 0.8004 (pp30) REVERT: H 130 TYR cc_start: 0.8660 (m-80) cc_final: 0.8401 (m-80) REVERT: L 27 GLN cc_start: 0.8605 (pm20) cc_final: 0.8133 (pm20) REVERT: L 29 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9206 (pp) REVERT: L 87 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8578 (pp20) REVERT: L 129 GLN cc_start: 0.8615 (tp-100) cc_final: 0.8133 (tp40) REVERT: L 161 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8446 (tm-30) REVERT: L 168 TRP cc_start: 0.9460 (m-90) cc_final: 0.8877 (m-90) REVERT: L 180 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7379 (tpt) outliers start: 41 outliers final: 29 residues processed: 227 average time/residue: 0.1816 time to fit residues: 57.8003 Evaluate side-chains 234 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 51 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU 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 293 GLN 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 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 102 THR Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 138 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 12 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 36 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3775 r_free = 0.3775 target = 0.140937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111245 restraints weight = 10662.880| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.72 r_work: 0.3208 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5842 Z= 0.123 Angle : 0.685 8.388 7940 Z= 0.331 Chirality : 0.044 0.171 918 Planarity : 0.004 0.037 981 Dihedral : 4.432 16.239 794 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % 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: -0.30 (0.32), residues: 737 helix: 1.06 (0.34), residues: 253 sheet: 0.63 (0.42), residues: 166 loop : -1.74 (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 0.022 0.001 PHE A 292 TYR 0.022 0.002 TYR H 183 ARG 0.004 0.000 ARG L 160 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 271) hydrogen bonds : angle 4.50939 ( 753) SS BOND : bond 0.00394 ( 3) SS BOND : angle 0.74621 ( 6) covalent geometry : bond 0.00283 ( 5839) covalent geometry : angle 0.68528 ( 7934) *********************** 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 243 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8114 (m-30) cc_final: 0.7874 (m-30) REVERT: A 46 MET cc_start: 0.9034 (mtt) cc_final: 0.8750 (mtp) REVERT: A 50 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8083 (mttp) REVERT: A 141 TYR cc_start: 0.9005 (m-80) cc_final: 0.8310 (m-80) REVERT: A 167 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8233 (tt) REVERT: A 223 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8049 (mt) REVERT: H 3 GLN cc_start: 0.9055 (pp30) cc_final: 0.8025 (pp30) REVERT: H 90 ASP cc_start: 0.9101 (OUTLIER) cc_final: 0.8831 (m-30) REVERT: H 130 TYR cc_start: 0.8756 (m-80) cc_final: 0.8445 (m-10) REVERT: H 215 ASP cc_start: 0.8766 (t0) cc_final: 0.7805 (p0) REVERT: L 29 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9188 (pp) REVERT: L 85 GLN cc_start: 0.7388 (tm-30) cc_final: 0.6827 (tm-30) REVERT: L 129 GLN cc_start: 0.8550 (tp-100) cc_final: 0.7887 (tp40) REVERT: L 160 ARG cc_start: 0.8455 (ptm-80) cc_final: 0.7498 (ptm-80) REVERT: L 161 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8385 (tm-30) REVERT: L 168 TRP cc_start: 0.9469 (m-90) cc_final: 0.8898 (m-90) REVERT: L 180 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7470 (tpt) outliers start: 35 outliers final: 21 residues processed: 218 average time/residue: 0.1350 time to fit residues: 40.2175 Evaluate side-chains 229 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 68 GLN Chi-restraints excluded: chain A residue 71 ILE 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 137 LEU Chi-restraints excluded: chain A residue 167 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 246 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 102 THR Chi-restraints excluded: chain L residue 138 VAL 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: 4.9990 chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 1 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.139669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110061 restraints weight = 10731.891| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.68 r_work: 0.3212 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5842 Z= 0.139 Angle : 0.679 9.840 7940 Z= 0.331 Chirality : 0.044 0.177 918 Planarity : 0.004 0.033 981 Dihedral : 4.416 16.264 794 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.64 % Allowed : 28.13 % 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: -0.20 (0.32), residues: 737 helix: 1.17 (0.34), residues: 253 sheet: 0.63 (0.42), residues: 166 loop : -1.68 (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 0.017 0.001 PHE A 292 TYR 0.022 0.002 TYR H 183 ARG 0.002 0.000 ARG L 160 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 271) hydrogen bonds : angle 4.45932 ( 753) SS BOND : bond 0.00259 ( 3) SS BOND : angle 0.63210 ( 6) covalent geometry : bond 0.00327 ( 5839) covalent geometry : angle 0.67903 ( 7934) *********************** 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 258 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8131 (m-30) cc_final: 0.7893 (m-30) REVERT: A 46 MET cc_start: 0.9036 (mtt) cc_final: 0.8748 (mtp) REVERT: A 50 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8150 (mttp) REVERT: A 141 TYR cc_start: 0.9003 (m-80) cc_final: 0.8232 (m-80) REVERT: A 167 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8223 (tt) REVERT: A 176 LEU cc_start: 0.8680 (tt) cc_final: 0.8250 (tt) REVERT: A 223 ILE cc_start: 0.8318 (mt) cc_final: 0.8050 (mt) REVERT: A 246 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7840 (mm) REVERT: H 3 GLN cc_start: 0.9085 (pp30) cc_final: 0.8041 (pp30) REVERT: H 90 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8837 (m-30) REVERT: H 117 LEU cc_start: 0.9414 (tp) cc_final: 0.9178 (tt) REVERT: H 130 TYR cc_start: 0.8784 (m-80) cc_final: 0.8536 (m-10) REVERT: H 215 ASP cc_start: 0.8695 (t0) cc_final: 0.7755 (p0) REVERT: L 29 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9207 (pp) REVERT: L 87 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8706 (pp20) REVERT: L 110 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8239 (mp0) REVERT: L 129 GLN cc_start: 0.8587 (tp-100) cc_final: 0.7996 (tp40) REVERT: L 161 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8340 (tm-30) REVERT: L 168 TRP cc_start: 0.9441 (m-90) cc_final: 0.8856 (m-90) REVERT: L 180 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7582 (tpt) outliers start: 30 outliers final: 19 residues processed: 238 average time/residue: 0.1344 time to fit residues: 43.6915 Evaluate side-chains 236 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 51 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 167 LEU 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 A residue 301 ILE 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 87 GLU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 164 VAL 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: 0.6980 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 chunk 65 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.140000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110320 restraints weight = 10669.363| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.70 r_work: 0.3217 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5842 Z= 0.134 Angle : 0.693 9.245 7940 Z= 0.337 Chirality : 0.044 0.183 918 Planarity : 0.004 0.036 981 Dihedral : 4.467 21.491 794 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 4.95 % Allowed : 28.59 % Favored : 66.46 % 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: -0.18 (0.32), residues: 737 helix: 1.14 (0.34), residues: 258 sheet: 0.70 (0.43), residues: 165 loop : -1.70 (0.34), residues: 314 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 0.022 0.002 TYR H 183 ARG 0.002 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 271) hydrogen bonds : angle 4.45236 ( 753) SS BOND : bond 0.00276 ( 3) SS BOND : angle 0.60114 ( 6) covalent geometry : bond 0.00318 ( 5839) covalent geometry : angle 0.69352 ( 7934) *********************** 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 250 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8115 (m-30) cc_final: 0.7888 (m-30) REVERT: A 50 LYS cc_start: 0.8584 (mmmt) cc_final: 0.8145 (mttp) REVERT: A 141 TYR cc_start: 0.8995 (m-80) cc_final: 0.8230 (m-80) REVERT: A 167 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8235 (tt) REVERT: A 176 LEU cc_start: 0.8785 (tt) cc_final: 0.8395 (tt) REVERT: A 183 TYR cc_start: 0.6114 (OUTLIER) cc_final: 0.5558 (m-10) REVERT: A 223 ILE cc_start: 0.8280 (mt) cc_final: 0.8023 (mt) REVERT: A 246 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7812 (mm) REVERT: H 3 GLN cc_start: 0.9043 (pp30) cc_final: 0.8012 (pp30) REVERT: H 90 ASP cc_start: 0.9078 (OUTLIER) cc_final: 0.8839 (m-30) REVERT: H 130 TYR cc_start: 0.8775 (m-80) cc_final: 0.8525 (m-10) REVERT: H 189 VAL cc_start: 0.9050 (p) cc_final: 0.8811 (m) REVERT: L 29 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9215 (pp) REVERT: L 87 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8675 (pp20) REVERT: L 129 GLN cc_start: 0.8542 (tp-100) cc_final: 0.7949 (tp40) REVERT: L 160 ARG cc_start: 0.8424 (ptm-80) cc_final: 0.7488 (ptm-80) REVERT: L 161 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8247 (tm-30) REVERT: L 168 TRP cc_start: 0.9447 (m-90) cc_final: 0.8865 (m-90) REVERT: L 180 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7575 (tpt) outliers start: 32 outliers final: 21 residues processed: 230 average time/residue: 0.1520 time to fit residues: 48.3961 Evaluate side-chains 243 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 51 ILE 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 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 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 A residue 301 ILE 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 102 THR 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: 0.1980 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.140657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111244 restraints weight = 10717.577| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.70 r_work: 0.3230 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5842 Z= 0.127 Angle : 0.697 10.248 7940 Z= 0.336 Chirality : 0.044 0.187 918 Planarity : 0.004 0.034 981 Dihedral : 4.419 16.587 794 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.64 % Allowed : 28.90 % Favored : 66.46 % 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: 1.23 (0.34), residues: 252 sheet: 0.77 (0.43), residues: 173 loop : -1.75 (0.34), residues: 312 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 0.021 0.001 PHE A 292 TYR 0.021 0.002 TYR H 183 ARG 0.003 0.000 ARG L 160 Details of bonding type rmsd hydrogen bonds : bond 0.03028 ( 271) hydrogen bonds : angle 4.43526 ( 753) SS BOND : bond 0.00226 ( 3) SS BOND : angle 0.60394 ( 6) covalent geometry : bond 0.00296 ( 5839) covalent geometry : angle 0.69712 ( 7934) *********************** 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 252 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8069 (m-30) cc_final: 0.7857 (m-30) REVERT: A 46 MET cc_start: 0.9014 (mtt) cc_final: 0.8684 (mtp) REVERT: A 50 LYS cc_start: 0.8567 (mmmt) cc_final: 0.8153 (mttp) REVERT: A 141 TYR cc_start: 0.8988 (m-80) cc_final: 0.8257 (m-80) REVERT: A 167 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8300 (tt) REVERT: A 176 LEU cc_start: 0.8799 (tt) cc_final: 0.8404 (tt) REVERT: A 183 TYR cc_start: 0.6106 (OUTLIER) cc_final: 0.5549 (m-10) REVERT: A 223 ILE cc_start: 0.8231 (mt) cc_final: 0.7979 (mt) REVERT: A 246 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7798 (mm) REVERT: H 3 GLN cc_start: 0.9039 (pp30) cc_final: 0.8006 (pp30) REVERT: H 90 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8820 (m-30) REVERT: H 100 TYR cc_start: 0.8888 (t80) cc_final: 0.8413 (t80) REVERT: H 130 TYR cc_start: 0.8753 (m-80) cc_final: 0.8493 (m-10) REVERT: H 189 VAL cc_start: 0.9071 (p) cc_final: 0.8871 (m) REVERT: L 29 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9229 (pp) REVERT: L 87 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8650 (pp20) REVERT: L 110 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8192 (mp0) REVERT: L 129 GLN cc_start: 0.8524 (tp-100) cc_final: 0.7922 (tp40) REVERT: L 160 ARG cc_start: 0.8418 (ptm-80) cc_final: 0.7417 (ptm-80) REVERT: L 161 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8121 (tm-30) REVERT: L 168 TRP cc_start: 0.9451 (m-90) cc_final: 0.8931 (m-90) REVERT: L 180 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7617 (tpt) outliers start: 30 outliers final: 18 residues processed: 231 average time/residue: 0.1313 time to fit residues: 41.6458 Evaluate side-chains 244 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 51 ILE Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 71 ILE 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 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 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 102 THR 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: 0.0000 chunk 58 optimal weight: 0.0980 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.141983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112685 restraints weight = 10777.671| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.73 r_work: 0.3235 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5842 Z= 0.119 Angle : 0.697 10.109 7940 Z= 0.336 Chirality : 0.044 0.202 918 Planarity : 0.004 0.034 981 Dihedral : 4.349 17.756 794 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.17 % Allowed : 29.83 % Favored : 66.00 % 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: -0.11 (0.32), residues: 737 helix: 1.22 (0.34), residues: 253 sheet: 0.81 (0.43), residues: 173 loop : -1.75 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.001 PHE A 292 TYR 0.019 0.002 TYR L 98 ARG 0.003 0.000 ARG L 160 Details of bonding type rmsd hydrogen bonds : bond 0.02929 ( 271) hydrogen bonds : angle 4.38804 ( 753) SS BOND : bond 0.00210 ( 3) SS BOND : angle 0.52808 ( 6) covalent geometry : bond 0.00275 ( 5839) covalent geometry : angle 0.69730 ( 7934) ********************** 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 253 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8044 (m-30) cc_final: 0.7833 (m-30) REVERT: A 46 MET cc_start: 0.9067 (mtt) cc_final: 0.8706 (mtp) REVERT: A 50 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8110 (mttp) REVERT: A 106 ASN cc_start: 0.8739 (m110) cc_final: 0.8041 (m-40) REVERT: A 141 TYR cc_start: 0.8894 (m-80) cc_final: 0.8276 (m-80) REVERT: A 176 LEU cc_start: 0.8739 (tt) cc_final: 0.8301 (tt) REVERT: A 183 TYR cc_start: 0.6072 (OUTLIER) cc_final: 0.5531 (m-10) REVERT: A 203 THR cc_start: 0.8266 (m) cc_final: 0.8050 (p) REVERT: A 223 ILE cc_start: 0.8183 (mt) cc_final: 0.7940 (mt) REVERT: H 3 GLN cc_start: 0.9010 (pp30) cc_final: 0.7969 (pp30) REVERT: H 90 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8741 (m-30) REVERT: H 130 TYR cc_start: 0.8741 (m-80) cc_final: 0.8486 (m-10) REVERT: H 189 VAL cc_start: 0.9154 (p) cc_final: 0.8923 (m) REVERT: L 29 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9217 (pp) REVERT: L 87 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8682 (pp20) REVERT: L 129 GLN cc_start: 0.8514 (tp-100) cc_final: 0.7935 (tp40) REVERT: L 161 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8035 (tm-30) REVERT: L 168 TRP cc_start: 0.9441 (m-90) cc_final: 0.8951 (m-90) REVERT: L 180 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7627 (tpt) outliers start: 27 outliers final: 19 residues processed: 235 average time/residue: 0.1251 time to fit residues: 40.7684 Evaluate side-chains 245 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 125 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 183 TYR 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 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 102 THR Chi-restraints excluded: chain L residue 164 VAL 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: 0.9980 chunk 67 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 0.0870 chunk 20 optimal weight: 10.0000 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN H 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111784 restraints weight = 10714.618| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.65 r_work: 0.3241 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5842 Z= 0.125 Angle : 0.701 9.884 7940 Z= 0.338 Chirality : 0.044 0.204 918 Planarity : 0.004 0.034 981 Dihedral : 4.328 16.957 794 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.02 % Allowed : 29.98 % Favored : 66.00 % 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 (0.32), residues: 737 helix: 1.31 (0.34), residues: 252 sheet: 0.70 (0.42), residues: 183 loop : -1.70 (0.35), residues: 302 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 0.019 0.002 TYR H 183 ARG 0.003 0.000 ARG L 160 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 271) hydrogen bonds : angle 4.36779 ( 753) SS BOND : bond 0.00248 ( 3) SS BOND : angle 0.56813 ( 6) covalent geometry : bond 0.00293 ( 5839) covalent geometry : angle 0.70080 ( 7934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3237.20 seconds wall clock time: 57 minutes 13.14 seconds (3433.14 seconds total)