Starting phenix.real_space_refine on Tue Aug 4 18:34:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hrx_34981/08_2026/8hrx_34981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hrx_34981/08_2026/8hrx_34981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hrx_34981/08_2026/8hrx_34981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hrx_34981/08_2026/8hrx_34981.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hrx_34981/08_2026/8hrx_34981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hrx_34981/08_2026/8hrx_34981.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 3872 2.51 5 N 973 2.21 5 O 1125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6013 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2322 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 16, 'TRANS': 285} Chain: "B" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 371 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 7, 'TRANS': 39} Chain: "H" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1661 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 14, 'TRANS': 204} Chain: "L" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1659 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 9, 'TRANS': 202} Time building chain proxies: 1.45, per 1000 atoms: 0.24 Number of scatterers: 6013 At special positions: 0 Unit cell: (74.7, 68.06, 144.42, 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 1125 8.00 N 973 7.00 C 3872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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: 0.46 Conformation dependent library (CDL) restraints added in 228.8 milliseconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1442 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 11 sheets defined 34.0% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 21 through 44 Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 58 through 84 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.906A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 143 Proline residue: A 135 - end of helix removed outlier: 3.891A pdb=" N ARG A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 180 removed outlier: 3.603A pdb=" N VAL A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 211 removed outlier: 3.604A pdb=" N GLY A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 4.150A pdb=" N ALA A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 218' Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 259 removed outlier: 3.638A pdb=" N ARG A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 253 " --> pdb=" O ARG A 249 " (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 311 Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.618A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.601A pdb=" N VAL H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.590A pdb=" N TYR H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 125 through 129 removed outlier: 4.074A pdb=" N LEU H 129 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR H 180 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 125 through 129 removed outlier: 4.074A pdb=" N LEU H 129 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR H 180 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 156 through 158 removed outlier: 3.667A pdb=" N LYS H 213 " --> pdb=" O CYS H 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.729A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS L 39 " --> pdb=" O THR L 43 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N THR L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.726A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL L 132 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER L 177 " --> pdb=" O CYS L 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.726A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 145 through 148 removed outlier: 3.540A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA L 196 " --> pdb=" O ILE L 205 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE L 205 " --> pdb=" O ALA L 196 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 846 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: 0.93 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1804 1.34 - 1.46: 1151 1.46 - 1.58: 3145 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 6165 Sorted by residual: bond pdb=" CA SER H 21 " pdb=" C SER H 21 " ideal model delta sigma weight residual 1.522 1.550 -0.027 1.19e-02 7.06e+03 5.21e+00 bond pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.21e-02 6.83e+03 3.96e+00 bond pdb=" CA MET H 20 " pdb=" C MET H 20 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.20e-02 6.94e+03 3.66e+00 bond pdb=" CA LYS H 19 " pdb=" C LYS H 19 " ideal model delta sigma weight residual 1.521 1.543 -0.022 1.24e-02 6.50e+03 3.20e+00 bond pdb=" C SER L 208 " pdb=" O SER L 208 " ideal model delta sigma weight residual 1.236 1.216 0.020 1.21e-02 6.83e+03 2.77e+00 ... (remaining 6160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 8244 2.39 - 4.79: 118 4.79 - 7.18: 18 7.18 - 9.57: 4 9.57 - 11.96: 2 Bond angle restraints: 8386 Sorted by residual: angle pdb=" N VAL A 187 " pdb=" CA VAL A 187 " pdb=" C VAL A 187 " ideal model delta sigma weight residual 110.72 116.90 -6.18 1.01e+00 9.80e-01 3.74e+01 angle pdb=" N LYS L 207 " pdb=" CA LYS L 207 " pdb=" C LYS L 207 " ideal model delta sigma weight residual 108.76 99.12 9.64 1.69e+00 3.50e-01 3.25e+01 angle pdb=" N ILE A 188 " pdb=" CA ILE A 188 " pdb=" C ILE A 188 " ideal model delta sigma weight residual 110.62 115.29 -4.67 1.02e+00 9.61e-01 2.10e+01 angle pdb=" N ALA A 217 " pdb=" CA ALA A 217 " pdb=" C ALA A 217 " ideal model delta sigma weight residual 113.16 118.52 -5.36 1.24e+00 6.50e-01 1.87e+01 angle pdb=" N PHE A 216 " pdb=" CA PHE A 216 " pdb=" C PHE A 216 " ideal model delta sigma weight residual 111.36 116.02 -4.66 1.09e+00 8.42e-01 1.83e+01 ... (remaining 8381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 3131 17.51 - 35.03: 403 35.03 - 52.54: 111 52.54 - 70.06: 13 70.06 - 87.57: 7 Dihedral angle restraints: 3665 sinusoidal: 1412 harmonic: 2253 Sorted by residual: dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual -86.00 -6.91 -79.09 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS H 145 " pdb=" SG CYS H 145 " pdb=" SG CYS H 200 " pdb=" CB CYS H 200 " ideal model delta sinusoidal sigma weight residual 93.00 38.53 54.47 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CA ALA H 92 " pdb=" C ALA H 92 " pdb=" N VAL H 93 " pdb=" CA VAL H 93 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 805 0.059 - 0.118: 140 0.118 - 0.176: 12 0.176 - 0.235: 1 0.235 - 0.294: 1 Chirality restraints: 959 Sorted by residual: chirality pdb=" CA LYS L 207 " pdb=" N LYS L 207 " pdb=" C LYS L 207 " pdb=" CB LYS L 207 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ALA A 217 " pdb=" N ALA A 217 " pdb=" C ALA A 217 " pdb=" CB ALA A 217 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU A 228 " pdb=" CB LEU A 228 " pdb=" CD1 LEU A 228 " pdb=" CD2 LEU A 228 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 956 not shown) Planarity restraints: 1047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 188 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO H 189 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 189 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 189 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 94 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO L 95 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 127 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.06e+00 pdb=" N PRO H 128 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO H 128 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 128 " 0.020 5.00e-02 4.00e+02 ... (remaining 1044 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 12 2.35 - 2.99: 3144 2.99 - 3.62: 8889 3.62 - 4.26: 13333 4.26 - 4.90: 23120 Nonbonded interactions: 48498 Sorted by model distance: nonbonded pdb=" O MET A 218 " pdb=" O THR A 219 " model vdw 1.709 3.040 nonbonded pdb=" CE MET H 20 " pdb=" CE MET H 81 " model vdw 1.734 3.880 nonbonded pdb=" N GLU L 187 " pdb=" OE1 GLU L 187 " model vdw 2.177 3.120 nonbonded pdb=" O GLY H 42 " pdb=" CG LYS H 43 " model vdw 2.212 3.440 nonbonded pdb=" OD1 ASN L 31 " pdb=" OG1 THR L 51 " model vdw 2.269 3.040 ... (remaining 48493 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: 2.060 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 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 0.043 6169 Z= 0.158 Angle : 0.702 11.963 8394 Z= 0.377 Chirality : 0.045 0.294 959 Planarity : 0.004 0.040 1047 Dihedral : 16.539 87.569 2211 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.61 % Favored : 93.13 % Rotamer: Outliers : 3.52 % Allowed : 31.57 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.31), residues: 772 helix: 1.63 (0.33), residues: 251 sheet: -0.23 (0.41), residues: 188 loop : -1.11 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 53 TYR 0.014 0.001 TYR L 173 PHE 0.007 0.001 PHE A 285 TRP 0.010 0.001 TRP H 159 HIS 0.001 0.000 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 ( 6165) covalent geometry : angle 0.70035 / 0.38 ( 8386) SS BOND : bond 0.00357 / 0.17 ( 4) SS BOND : angle 1.49375 / 0.90 ( 8) hydrogen bonds : bond 0.17545 / 10.14 ( 279) hydrogen bonds : angle 7.49067 / 5.42 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.230 Fit side-chains REVERT: L 207 LYS cc_start: 0.7120 (mmmm) cc_final: 0.6888 (mmmm) outliers start: 24 outliers final: 21 residues processed: 170 average time/residue: 0.3444 time to fit residues: 63.0109 Evaluate side-chains 166 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 200 THR Chi-restraints excluded: chain L residue 205 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 chunk 51 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.0273 > 50:) chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 ASN A 209 ASN A 262 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN L 210 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.127878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.099481 restraints weight = 9412.214| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.72 r_work: 0.3047 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6169 Z= 0.136 Angle : 0.636 9.548 8394 Z= 0.317 Chirality : 0.043 0.134 959 Planarity : 0.004 0.040 1047 Dihedral : 5.807 45.752 858 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.74 % Favored : 93.13 % Rotamer: Outliers : 4.99 % Allowed : 28.34 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.31), residues: 772 helix: 1.62 (0.32), residues: 260 sheet: -0.29 (0.39), residues: 206 loop : -1.19 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 53 TYR 0.009 0.001 TYR H 50 PHE 0.008 0.001 PHE A 77 TRP 0.006 0.001 TRP H 47 HIS 0.001 0.000 HIS H 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 6165) covalent geometry : angle 0.63342 / 0.32 ( 8386) SS BOND : bond 0.00511 / 0.25 ( 4) SS BOND : angle 2.04766 / 1.30 ( 8) hydrogen bonds : bond 0.04330 / 2.85 ( 279) hydrogen bonds : angle 5.15999 / 3.69 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.289 Fit side-chains REVERT: A 55 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8511 (mp) REVERT: A 180 ARG cc_start: 0.6799 (mtt90) cc_final: 0.6370 (mtt-85) REVERT: A 182 GLN cc_start: 0.6994 (pm20) cc_final: 0.5974 (pt0) REVERT: A 183 TYR cc_start: 0.6617 (m-80) cc_final: 0.6141 (m-80) REVERT: A 218 MET cc_start: 0.6159 (mmm) cc_final: 0.5888 (mmt) REVERT: A 228 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8609 (mp) REVERT: H 73 ASP cc_start: 0.8420 (t0) cc_final: 0.8190 (t0) REVERT: L 61 ARG cc_start: 0.8740 (ptt-90) cc_final: 0.8374 (ptt-90) REVERT: L 79 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8293 (mp0) REVERT: L 207 LYS cc_start: 0.7869 (mmmm) cc_final: 0.7579 (mmmm) outliers start: 34 outliers final: 15 residues processed: 182 average time/residue: 0.3540 time to fit residues: 69.1953 Evaluate side-chains 157 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.0270 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 ASN A 209 ASN A 262 ASN L 6 GLN L 161 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.126176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098758 restraints weight = 9228.253| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.66 r_work: 0.3042 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6169 Z= 0.132 Angle : 0.639 10.635 8394 Z= 0.313 Chirality : 0.043 0.134 959 Planarity : 0.004 0.040 1047 Dihedral : 4.826 38.350 839 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.87 % Favored : 93.01 % Rotamer: Outliers : 5.14 % Allowed : 28.34 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.31), residues: 772 helix: 1.67 (0.32), residues: 259 sheet: -0.37 (0.39), residues: 206 loop : -1.20 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 61 TYR 0.008 0.001 TYR A 146 PHE 0.007 0.001 PHE L 98 TRP 0.005 0.001 TRP H 47 HIS 0.001 0.000 HIS H 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6165) covalent geometry : angle 0.63681 / 0.31 ( 8386) SS BOND : bond 0.00460 / 0.22 ( 4) SS BOND : angle 1.97893 / 1.10 ( 8) hydrogen bonds : bond 0.04057 / 2.70 ( 279) hydrogen bonds : angle 4.71347 / 3.35 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.256 Fit side-chains REVERT: A 55 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8492 (mp) REVERT: A 184 MET cc_start: 0.3772 (OUTLIER) cc_final: 0.3545 (ttt) REVERT: H 73 ASP cc_start: 0.8520 (t0) cc_final: 0.8251 (t0) REVERT: L 61 ARG cc_start: 0.8733 (ptt-90) cc_final: 0.8419 (ptt-90) REVERT: L 79 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8348 (mp0) REVERT: L 207 LYS cc_start: 0.8023 (mmmm) cc_final: 0.7736 (mmmm) outliers start: 35 outliers final: 17 residues processed: 170 average time/residue: 0.3883 time to fit residues: 70.3651 Evaluate side-chains 150 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 182 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 62 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN A 262 ASN L 161 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.098610 restraints weight = 9215.228| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.68 r_work: 0.3046 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6169 Z= 0.128 Angle : 0.624 8.618 8394 Z= 0.308 Chirality : 0.042 0.132 959 Planarity : 0.004 0.041 1047 Dihedral : 4.719 38.636 837 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.87 % Favored : 93.01 % Rotamer: Outliers : 4.41 % Allowed : 28.78 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.31), residues: 772 helix: 1.66 (0.32), residues: 259 sheet: -0.44 (0.38), residues: 206 loop : -1.18 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 61 TYR 0.011 0.001 TYR A 183 PHE 0.007 0.001 PHE L 98 TRP 0.005 0.001 TRP L 163 HIS 0.001 0.000 HIS H 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 6165) covalent geometry : angle 0.62267 / 0.31 ( 8386) SS BOND : bond 0.00411 / 0.20 ( 4) SS BOND : angle 1.46359 / 0.87 ( 8) hydrogen bonds : bond 0.03885 / 2.60 ( 279) hydrogen bonds : angle 4.45756 / 3.16 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.236 Fit side-chains REVERT: A 55 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8447 (mp) REVERT: A 180 ARG cc_start: 0.6952 (mtt90) cc_final: 0.6540 (mtt-85) REVERT: A 182 GLN cc_start: 0.7170 (pm20) cc_final: 0.6180 (pt0) REVERT: A 183 TYR cc_start: 0.6706 (m-80) cc_final: 0.6243 (m-80) REVERT: A 219 THR cc_start: 0.7523 (m) cc_final: 0.7000 (p) REVERT: H 73 ASP cc_start: 0.8571 (t0) cc_final: 0.8288 (t0) REVERT: L 79 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8342 (mp0) outliers start: 30 outliers final: 18 residues processed: 163 average time/residue: 0.3644 time to fit residues: 63.5757 Evaluate side-chains 157 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 182 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 27 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN A 262 ASN L 161 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.099599 restraints weight = 9300.121| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.74 r_work: 0.3056 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6169 Z= 0.118 Angle : 0.624 11.430 8394 Z= 0.305 Chirality : 0.042 0.130 959 Planarity : 0.004 0.041 1047 Dihedral : 4.706 38.715 837 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.26 % Allowed : 29.37 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.31), residues: 772 helix: 1.66 (0.32), residues: 259 sheet: -0.40 (0.38), residues: 207 loop : -1.15 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 53 TYR 0.012 0.001 TYR A 183 PHE 0.007 0.001 PHE L 98 TRP 0.005 0.001 TRP H 104 HIS 0.001 0.000 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 6165) covalent geometry : angle 0.62295 / 0.30 ( 8386) SS BOND : bond 0.00359 / 0.18 ( 4) SS BOND : angle 1.41950 / 0.78 ( 8) hydrogen bonds : bond 0.03776 / 2.54 ( 279) hydrogen bonds : angle 4.37825 / 3.07 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.234 Fit side-chains REVERT: A 55 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8426 (mp) REVERT: A 96 CYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8266 (m) REVERT: A 219 THR cc_start: 0.7111 (m) cc_final: 0.6702 (p) REVERT: B 18 GLN cc_start: 0.9411 (OUTLIER) cc_final: 0.9149 (mp10) REVERT: H 73 ASP cc_start: 0.8558 (t0) cc_final: 0.8270 (t0) REVERT: L 79 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8444 (mp0) outliers start: 29 outliers final: 18 residues processed: 166 average time/residue: 0.3701 time to fit residues: 65.7822 Evaluate side-chains 161 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 182 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.0070 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN A 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.098856 restraints weight = 9198.655| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.70 r_work: 0.3048 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6169 Z= 0.131 Angle : 0.624 8.226 8394 Z= 0.310 Chirality : 0.043 0.131 959 Planarity : 0.004 0.041 1047 Dihedral : 4.736 38.796 837 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.85 % Allowed : 29.96 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.31), residues: 772 helix: 1.63 (0.32), residues: 259 sheet: -0.40 (0.38), residues: 207 loop : -1.16 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 53 TYR 0.009 0.001 TYR L 87 PHE 0.008 0.001 PHE L 98 TRP 0.006 0.001 TRP L 163 HIS 0.001 0.000 HIS H 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 6165) covalent geometry : angle 0.62307 / 0.31 ( 8386) SS BOND : bond 0.00435 / 0.21 ( 4) SS BOND : angle 1.25342 / 0.76 ( 8) hydrogen bonds : bond 0.03832 / 2.58 ( 279) hydrogen bonds : angle 4.28571 / 3.00 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.233 Fit side-chains REVERT: A 55 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8441 (mp) REVERT: A 96 CYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8277 (m) REVERT: H 73 ASP cc_start: 0.8593 (t0) cc_final: 0.8302 (t0) REVERT: L 79 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8407 (mp0) outliers start: 33 outliers final: 18 residues processed: 161 average time/residue: 0.3738 time to fit residues: 64.4912 Evaluate side-chains 149 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 182 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN A 262 ASN L 161 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.096976 restraints weight = 9288.052| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.74 r_work: 0.3015 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6169 Z= 0.163 Angle : 0.667 12.050 8394 Z= 0.326 Chirality : 0.044 0.141 959 Planarity : 0.004 0.040 1047 Dihedral : 4.921 39.611 837 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.26 % Allowed : 30.84 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.31), residues: 772 helix: 1.56 (0.32), residues: 260 sheet: -0.41 (0.38), residues: 207 loop : -1.20 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 53 TYR 0.014 0.001 TYR A 183 PHE 0.010 0.001 PHE H 102 TRP 0.008 0.001 TRP L 163 HIS 0.001 0.001 HIS H 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 6165) covalent geometry : angle 0.66402 / 0.32 ( 8386) SS BOND : bond 0.00490 / 0.24 ( 4) SS BOND : angle 2.01403 / 1.09 ( 8) hydrogen bonds : bond 0.04086 / 2.77 ( 279) hydrogen bonds : angle 4.28594 / 3.02 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.239 Fit side-chains REVERT: A 55 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8495 (mp) REVERT: A 96 CYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8324 (m) REVERT: B 18 GLN cc_start: 0.9449 (mt0) cc_final: 0.9224 (mp10) REVERT: H 73 ASP cc_start: 0.8669 (t0) cc_final: 0.8404 (t0) REVERT: L 17 ASP cc_start: 0.8469 (t0) cc_final: 0.7857 (t0) REVERT: L 79 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8433 (mp0) REVERT: L 144 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8422 (pt) outliers start: 29 outliers final: 21 residues processed: 169 average time/residue: 0.3678 time to fit residues: 66.5915 Evaluate side-chains 159 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL 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 245 CYS Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 182 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 144 ILE Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 194 CYS Chi-restraints excluded: chain L residue 205 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN A 262 ASN B 18 GLN H 40 ASN L 161 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.122759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.095352 restraints weight = 9397.237| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.66 r_work: 0.2989 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6169 Z= 0.204 Angle : 0.704 9.073 8394 Z= 0.353 Chirality : 0.045 0.159 959 Planarity : 0.004 0.039 1047 Dihedral : 5.249 38.919 837 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 5.14 % Allowed : 31.13 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.31), residues: 772 helix: 1.42 (0.32), residues: 260 sheet: -0.49 (0.37), residues: 207 loop : -1.28 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 53 TYR 0.012 0.001 TYR L 91 PHE 0.014 0.001 PHE H 102 TRP 0.010 0.001 TRP L 163 HIS 0.002 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 ( 6165) covalent geometry : angle 0.70247 / 0.35 ( 8386) SS BOND : bond 0.00493 / 0.24 ( 4) SS BOND : angle 1.45693 / 0.89 ( 8) hydrogen bonds : bond 0.04502 / 3.06 ( 279) hydrogen bonds : angle 4.36885 / 3.08 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.245 Fit side-chains REVERT: A 55 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8585 (mp) REVERT: A 96 CYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8399 (m) REVERT: B 29 ASN cc_start: 0.8388 (p0) cc_final: 0.8165 (p0) REVERT: H 73 ASP cc_start: 0.8754 (t0) cc_final: 0.8510 (t0) REVERT: L 79 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8520 (mp0) outliers start: 35 outliers final: 19 residues processed: 162 average time/residue: 0.4109 time to fit residues: 70.8846 Evaluate side-chains 157 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 182 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 36 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 39 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN A 293 GLN H 40 ASN H 196 GLN L 161 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.097154 restraints weight = 9277.042| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.74 r_work: 0.3009 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6169 Z= 0.138 Angle : 0.690 11.807 8394 Z= 0.337 Chirality : 0.044 0.141 959 Planarity : 0.004 0.038 1047 Dihedral : 5.207 39.118 837 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.82 % Allowed : 32.45 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.31), residues: 772 helix: 1.46 (0.32), residues: 259 sheet: -0.52 (0.37), residues: 207 loop : -1.27 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 53 TYR 0.015 0.001 TYR A 146 PHE 0.010 0.001 PHE L 118 TRP 0.008 0.001 TRP H 159 HIS 0.002 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6165) covalent geometry : angle 0.68952 / 0.34 ( 8386) SS BOND : bond 0.00348 / 0.17 ( 4) SS BOND : angle 1.35091 / 0.77 ( 8) hydrogen bonds : bond 0.04098 / 2.79 ( 279) hydrogen bonds : angle 4.31784 / 3.04 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.236 Fit side-chains REVERT: A 55 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8534 (mp) REVERT: A 96 CYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8383 (m) REVERT: H 73 ASP cc_start: 0.8734 (t0) cc_final: 0.8466 (t0) REVERT: L 17 ASP cc_start: 0.8547 (t0) cc_final: 0.8009 (t0) REVERT: L 61 ARG cc_start: 0.8783 (ptt-90) cc_final: 0.8574 (ptt-90) REVERT: L 79 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8463 (mp0) outliers start: 26 outliers final: 17 residues processed: 162 average time/residue: 0.3766 time to fit residues: 65.1674 Evaluate side-chains 151 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 182 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 0.0030 chunk 39 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN A 262 ASN H 40 ASN L 161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.099050 restraints weight = 9216.200| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.70 r_work: 0.3027 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6169 Z= 0.134 Angle : 0.689 11.163 8394 Z= 0.340 Chirality : 0.044 0.149 959 Planarity : 0.004 0.038 1047 Dihedral : 5.087 38.243 837 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.52 % Allowed : 33.19 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.31), residues: 772 helix: 1.44 (0.32), residues: 260 sheet: -0.50 (0.37), residues: 207 loop : -1.17 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 53 TYR 0.014 0.001 TYR A 146 PHE 0.023 0.001 PHE H 29 TRP 0.009 0.001 TRP H 159 HIS 0.001 0.000 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 6165) covalent geometry : angle 0.68796 / 0.34 ( 8386) SS BOND : bond 0.00311 / 0.15 ( 4) SS BOND : angle 1.27231 / 0.69 ( 8) hydrogen bonds : bond 0.03978 / 2.70 ( 279) hydrogen bonds : angle 4.28021 / 3.02 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.252 Fit side-chains REVERT: A 55 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8443 (mp) REVERT: A 96 CYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8249 (m) REVERT: H 73 ASP cc_start: 0.8679 (t0) cc_final: 0.8365 (t0) REVERT: L 61 ARG cc_start: 0.8713 (ptt-90) cc_final: 0.8512 (ptt-90) REVERT: L 79 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8457 (mp0) outliers start: 24 outliers final: 17 residues processed: 158 average time/residue: 0.4111 time to fit residues: 69.2914 Evaluate side-chains 157 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 182 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 205 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 47 optimal weight: 0.0470 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 61 optimal weight: 0.0040 overall best weight: 0.4890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN H 196 GLN L 161 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099963 restraints weight = 9175.389| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.67 r_work: 0.3048 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6169 Z= 0.126 Angle : 0.680 14.705 8394 Z= 0.329 Chirality : 0.043 0.139 959 Planarity : 0.004 0.039 1047 Dihedral : 5.028 40.973 837 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.23 % Allowed : 33.48 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.31), residues: 772 helix: 1.45 (0.32), residues: 259 sheet: -0.44 (0.38), residues: 202 loop : -1.16 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 53 TYR 0.013 0.001 TYR A 146 PHE 0.017 0.001 PHE H 29 TRP 0.009 0.001 TRP H 159 HIS 0.001 0.000 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 6165) covalent geometry : angle 0.67932 / 0.33 ( 8386) SS BOND : bond 0.00304 / 0.15 ( 4) SS BOND : angle 1.12388 / 0.69 ( 8) hydrogen bonds : bond 0.03801 / 2.57 ( 279) hydrogen bonds : angle 4.26590 / 3.00 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2530.35 seconds wall clock time: 44 minutes 2.80 seconds (2642.80 seconds total)