Starting phenix.real_space_refine on Thu Jun 5 11:01:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hrx_34981/06_2025/8hrx_34981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hrx_34981/06_2025/8hrx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hrx_34981/06_2025/8hrx_34981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hrx_34981/06_2025/8hrx_34981.map" model { file = "/net/cci-nas-00/data/ceres_data/8hrx_34981/06_2025/8hrx_34981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hrx_34981/06_2025/8hrx_34981.cif" } resolution = 2.89 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 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 4.94, per 1000 atoms: 0.82 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: 1.51 Conformation dependent library (CDL) restraints added in 933.9 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: 0.81 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: 1.74 Time building geometry restraints manager: 1.78 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: 2.330 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.680 Find NCS groups from input model: 0.070 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:15.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.31), residues: 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 TRP 0.010 0.001 TRP H 159 HIS 0.001 0.000 HIS L 198 PHE 0.007 0.001 PHE A 285 TYR 0.014 0.001 TYR L 173 ARG 0.004 0.000 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.17545 ( 279) hydrogen bonds : angle 7.49067 ( 846) SS BOND : bond 0.00357 ( 4) SS BOND : angle 1.49375 ( 8) covalent geometry : bond 0.00297 ( 6165) covalent geometry : angle 0.70035 ( 8386) *********************** 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 : 0.918 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: 0.7604 time to fit residues: 138.5789 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 : 0.634 ------------------------------------------------------------------------------- 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 64 optimal weight: 0.2980 chunk 57 optimal weight: 0.0980 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3569 r_free = 0.3569 target = 0.129718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.102013 restraints weight = 9175.737| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.65 r_work: 0.3079 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6169 Z= 0.118 Angle : 0.622 8.800 8394 Z= 0.309 Chirality : 0.042 0.131 959 Planarity : 0.004 0.041 1047 Dihedral : 5.672 46.254 858 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.74 % Favored : 93.13 % Rotamer: Outliers : 4.41 % Allowed : 28.49 % Favored : 67.11 % 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: 0.05 (0.31), residues: 772 helix: 1.64 (0.32), residues: 260 sheet: -0.22 (0.40), residues: 203 loop : -1.15 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 47 HIS 0.001 0.000 HIS H 41 PHE 0.007 0.001 PHE A 77 TYR 0.009 0.001 TYR A 307 ARG 0.002 0.000 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 279) hydrogen bonds : angle 5.20323 ( 846) SS BOND : bond 0.00433 ( 4) SS BOND : angle 1.85518 ( 8) covalent geometry : bond 0.00244 ( 6165) covalent geometry : angle 0.61939 ( 8386) *********************** 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 185 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 1.114 Fit side-chains REVERT: A 55 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8473 (mp) REVERT: A 218 MET cc_start: 0.6042 (mmm) cc_final: 0.5734 (mmt) REVERT: H 73 ASP cc_start: 0.8326 (t0) cc_final: 0.8109 (t0) REVERT: L 61 ARG cc_start: 0.8724 (ptt-90) cc_final: 0.8369 (ptt-90) REVERT: L 79 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8291 (mp0) REVERT: L 207 LYS cc_start: 0.7762 (mmmm) cc_final: 0.7479 (mmmm) outliers start: 30 outliers final: 10 residues processed: 178 average time/residue: 0.7608 time to fit residues: 146.1396 Evaluate side-chains 153 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 H residue 2 VAL Chi-restraints excluded: chain H residue 71 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 180 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 10.0000 chunk 33 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 106 ASN A 209 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 34 ASN L 161 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096824 restraints weight = 9316.842| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.75 r_work: 0.3012 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6169 Z= 0.180 Angle : 0.673 11.022 8394 Z= 0.331 Chirality : 0.045 0.142 959 Planarity : 0.004 0.040 1047 Dihedral : 4.663 27.888 836 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.74 % Favored : 93.13 % Rotamer: Outliers : 5.29 % Allowed : 27.02 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.31), residues: 772 helix: 1.63 (0.33), residues: 259 sheet: -0.42 (0.38), residues: 206 loop : -1.22 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 163 HIS 0.002 0.001 HIS H 204 PHE 0.009 0.001 PHE A 285 TYR 0.011 0.001 TYR L 91 ARG 0.002 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 279) hydrogen bonds : angle 4.77715 ( 846) SS BOND : bond 0.00863 ( 4) SS BOND : angle 2.48411 ( 8) covalent geometry : bond 0.00422 ( 6165) covalent geometry : angle 0.66877 ( 8386) *********************** 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 190 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.690 Fit side-chains REVERT: A 55 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8531 (mp) REVERT: A 96 CYS cc_start: 0.8623 (m) cc_final: 0.8328 (m) REVERT: H 73 ASP cc_start: 0.8497 (t0) cc_final: 0.8223 (t0) REVERT: L 61 ARG cc_start: 0.8693 (ptt-90) cc_final: 0.8313 (ptt-90) REVERT: L 79 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8319 (mp0) REVERT: L 207 LYS cc_start: 0.7990 (mmmm) cc_final: 0.7702 (mmmm) outliers start: 36 outliers final: 20 residues processed: 176 average time/residue: 0.8457 time to fit residues: 158.8371 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 : 0.725 ------------------------------------------------------------------------------- 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 215 MET Chi-restraints excluded: chain A residue 223 ILE 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 121 THR 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 58 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 210 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 10 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 262 ASN A 293 GLN B 18 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 161 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.093740 restraints weight = 9430.543| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.69 r_work: 0.2961 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6169 Z= 0.222 Angle : 0.687 10.511 8394 Z= 0.346 Chirality : 0.046 0.156 959 Planarity : 0.004 0.042 1047 Dihedral : 4.990 36.640 835 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.51 % Favored : 92.36 % Rotamer: Outliers : 6.02 % Allowed : 28.49 % Favored : 65.49 % 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: -0.26 (0.31), residues: 772 helix: 1.47 (0.32), residues: 259 sheet: -0.47 (0.37), residues: 207 loop : -1.36 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 163 HIS 0.003 0.001 HIS H 204 PHE 0.014 0.001 PHE H 102 TYR 0.013 0.002 TYR L 91 ARG 0.002 0.000 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 279) hydrogen bonds : angle 4.64869 ( 846) SS BOND : bond 0.00716 ( 4) SS BOND : angle 2.34936 ( 8) covalent geometry : bond 0.00525 ( 6165) covalent geometry : angle 0.68327 ( 8386) *********************** 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 191 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.638 Fit side-chains REVERT: A 55 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 96 CYS cc_start: 0.8713 (m) cc_final: 0.8427 (m) REVERT: A 218 MET cc_start: 0.6939 (mmt) cc_final: 0.6686 (mmt) REVERT: H 73 ASP cc_start: 0.8740 (t0) cc_final: 0.8481 (t0) REVERT: L 61 ARG cc_start: 0.8771 (ptt-90) cc_final: 0.8359 (ptt-90) REVERT: L 79 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8442 (mp0) outliers start: 41 outliers final: 20 residues processed: 174 average time/residue: 0.9006 time to fit residues: 166.7728 Evaluate side-chains 158 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 126 SER Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 152 ASP 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 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 121 THR 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 50 TYR Chi-restraints excluded: chain L residue 58 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 45 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 262 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 161 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096699 restraints weight = 9261.966| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.73 r_work: 0.3004 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6169 Z= 0.140 Angle : 0.661 11.882 8394 Z= 0.324 Chirality : 0.043 0.137 959 Planarity : 0.004 0.039 1047 Dihedral : 4.892 38.700 835 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.87 % Favored : 93.01 % Rotamer: Outliers : 5.14 % Allowed : 30.10 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.30), residues: 772 helix: 1.51 (0.32), residues: 259 sheet: -0.49 (0.37), residues: 207 loop : -1.36 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 163 HIS 0.002 0.001 HIS B 17 PHE 0.010 0.001 PHE L 118 TYR 0.011 0.001 TYR A 146 ARG 0.001 0.000 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 279) hydrogen bonds : angle 4.48942 ( 846) SS BOND : bond 0.00339 ( 4) SS BOND : angle 1.82658 ( 8) covalent geometry : bond 0.00321 ( 6165) covalent geometry : angle 0.65912 ( 8386) *********************** 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 182 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.642 Fit side-chains REVERT: A 55 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8475 (mp) REVERT: A 96 CYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8346 (m) REVERT: A 182 GLN cc_start: 0.7316 (pm20) cc_final: 0.6432 (pt0) REVERT: A 183 TYR cc_start: 0.6830 (m-80) cc_final: 0.6350 (m-80) REVERT: H 73 ASP cc_start: 0.8696 (t0) cc_final: 0.8411 (t0) REVERT: L 17 ASP cc_start: 0.8449 (t0) cc_final: 0.7828 (t0) REVERT: L 79 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8371 (mp0) REVERT: L 209 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7499 (t80) outliers start: 35 outliers final: 17 residues processed: 168 average time/residue: 0.7881 time to fit residues: 141.5279 Evaluate side-chains 157 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 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 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 121 THR 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 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 51 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 61 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 262 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3537 r_free = 0.3537 target = 0.126427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.098819 restraints weight = 9137.493| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.68 r_work: 0.3033 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6169 Z= 0.120 Angle : 0.628 7.775 8394 Z= 0.313 Chirality : 0.043 0.150 959 Planarity : 0.004 0.040 1047 Dihedral : 4.753 36.713 835 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.41 % Allowed : 30.25 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.31), residues: 772 helix: 1.52 (0.32), residues: 260 sheet: -0.50 (0.37), residues: 207 loop : -1.31 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 159 HIS 0.001 0.000 HIS B 17 PHE 0.011 0.001 PHE L 118 TYR 0.013 0.001 TYR A 146 ARG 0.002 0.000 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 279) hydrogen bonds : angle 4.38287 ( 846) SS BOND : bond 0.00331 ( 4) SS BOND : angle 1.44893 ( 8) covalent geometry : bond 0.00266 ( 6165) covalent geometry : angle 0.62695 ( 8386) *********************** 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 184 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.629 Fit side-chains REVERT: A 55 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8453 (mp) REVERT: A 96 CYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8306 (m) REVERT: A 182 GLN cc_start: 0.7305 (pm20) cc_final: 0.6462 (pt0) REVERT: A 183 TYR cc_start: 0.6784 (m-80) cc_final: 0.6325 (m-80) REVERT: A 221 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7780 (mm) REVERT: H 73 ASP cc_start: 0.8650 (t0) cc_final: 0.8335 (t0) REVERT: L 17 ASP cc_start: 0.8476 (t0) cc_final: 0.7890 (t0) REVERT: L 61 ARG cc_start: 0.8800 (ptt-90) cc_final: 0.8462 (ptt-90) REVERT: L 79 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8372 (mp0) REVERT: L 209 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7414 (t80) outliers start: 30 outliers final: 17 residues processed: 170 average time/residue: 0.8197 time to fit residues: 149.0745 Evaluate side-chains 160 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 131 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 221 LEU 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 147 VAL Chi-restraints excluded: chain H residue 182 MET Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 9 SER 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 209 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 0.0370 chunk 42 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 21 optimal weight: 3.9990 overall best weight: 0.4460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.099563 restraints weight = 9139.042| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.70 r_work: 0.3050 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6169 Z= 0.122 Angle : 0.654 12.450 8394 Z= 0.318 Chirality : 0.042 0.141 959 Planarity : 0.004 0.040 1047 Dihedral : 4.666 34.501 835 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.55 % Allowed : 31.13 % Favored : 64.32 % 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: -0.15 (0.31), residues: 772 helix: 1.56 (0.32), residues: 260 sheet: -0.45 (0.38), residues: 207 loop : -1.26 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 159 HIS 0.002 0.000 HIS B 17 PHE 0.010 0.001 PHE L 118 TYR 0.010 0.001 TYR A 146 ARG 0.005 0.000 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 279) hydrogen bonds : angle 4.29106 ( 846) SS BOND : bond 0.00481 ( 4) SS BOND : angle 1.65529 ( 8) covalent geometry : bond 0.00276 ( 6165) covalent geometry : angle 0.65265 ( 8386) *********************** 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 173 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.744 Fit side-chains REVERT: A 55 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8461 (mp) REVERT: A 96 CYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8286 (m) REVERT: A 182 GLN cc_start: 0.7352 (pm20) cc_final: 0.6540 (pt0) REVERT: A 183 TYR cc_start: 0.6766 (m-80) cc_final: 0.6330 (m-80) REVERT: B 29 ASN cc_start: 0.8286 (p0) cc_final: 0.8065 (p0) REVERT: H 73 ASP cc_start: 0.8664 (t0) cc_final: 0.8383 (t0) REVERT: L 79 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8382 (mp0) REVERT: L 209 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.7407 (t80) outliers start: 31 outliers final: 18 residues processed: 164 average time/residue: 0.7761 time to fit residues: 136.1383 Evaluate side-chains 158 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 167 LEU Chi-restraints excluded: chain A residue 184 MET 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 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 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 71 optimal weight: 0.0040 chunk 26 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 262 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 161 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.099256 restraints weight = 9184.108| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.70 r_work: 0.3034 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1796 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= 0.135 Angle : 0.673 11.303 8394 Z= 0.329 Chirality : 0.043 0.159 959 Planarity : 0.004 0.040 1047 Dihedral : 4.725 34.194 835 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.82 % Allowed : 32.01 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.31), residues: 772 helix: 1.55 (0.32), residues: 260 sheet: -0.44 (0.38), residues: 202 loop : -1.24 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 159 HIS 0.001 0.000 HIS B 17 PHE 0.011 0.001 PHE L 118 TYR 0.010 0.001 TYR L 87 ARG 0.004 0.000 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 279) hydrogen bonds : angle 4.28882 ( 846) SS BOND : bond 0.00373 ( 4) SS BOND : angle 1.78270 ( 8) covalent geometry : bond 0.00313 ( 6165) covalent geometry : angle 0.67067 ( 8386) *********************** 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 171 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.721 Fit side-chains REVERT: A 55 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8470 (mp) REVERT: A 96 CYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8267 (m) REVERT: A 182 GLN cc_start: 0.7375 (pm20) cc_final: 0.6567 (pt0) REVERT: A 183 TYR cc_start: 0.6777 (m-80) cc_final: 0.6363 (m-80) REVERT: B 29 ASN cc_start: 0.8323 (p0) cc_final: 0.8091 (p0) REVERT: H 73 ASP cc_start: 0.8610 (t0) cc_final: 0.8296 (t0) REVERT: L 17 ASP cc_start: 0.8473 (t0) cc_final: 0.7904 (t0) REVERT: L 53 ARG cc_start: 0.8359 (mmt-90) cc_final: 0.8071 (mmt-90) REVERT: L 79 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8399 (mp0) REVERT: L 209 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7381 (t80) outliers start: 26 outliers final: 19 residues processed: 162 average time/residue: 0.8093 time to fit residues: 140.2763 Evaluate side-chains 157 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 167 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 244 PHE 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 121 THR 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 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 0.0020 chunk 11 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 262 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 ASN H 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.098282 restraints weight = 9230.497| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.70 r_work: 0.3034 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6169 Z= 0.142 Angle : 0.675 8.616 8394 Z= 0.331 Chirality : 0.043 0.138 959 Planarity : 0.004 0.040 1047 Dihedral : 4.814 35.179 835 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.08 % Allowed : 33.04 % Favored : 63.88 % 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 (0.31), residues: 772 helix: 1.54 (0.32), residues: 259 sheet: -0.50 (0.38), residues: 202 loop : -1.23 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 159 HIS 0.001 0.000 HIS B 17 PHE 0.012 0.001 PHE L 118 TYR 0.010 0.001 TYR A 146 ARG 0.004 0.000 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 279) hydrogen bonds : angle 4.27447 ( 846) SS BOND : bond 0.00425 ( 4) SS BOND : angle 1.88549 ( 8) covalent geometry : bond 0.00332 ( 6165) covalent geometry : angle 0.67304 ( 8386) *********************** 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 163 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.691 Fit side-chains REVERT: A 55 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8490 (mp) REVERT: A 96 CYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8348 (m) REVERT: A 180 ARG cc_start: 0.6789 (mtt-85) cc_final: 0.6372 (mmt-90) REVERT: A 182 GLN cc_start: 0.7381 (pm20) cc_final: 0.6578 (pt0) REVERT: A 183 TYR cc_start: 0.6857 (m-80) cc_final: 0.6456 (m-80) REVERT: B 29 ASN cc_start: 0.8331 (p0) cc_final: 0.8116 (p0) REVERT: H 73 ASP cc_start: 0.8664 (t0) cc_final: 0.8381 (t0) REVERT: L 79 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8444 (mp0) REVERT: L 209 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7332 (t80) outliers start: 21 outliers final: 17 residues processed: 157 average time/residue: 0.8102 time to fit residues: 135.9486 Evaluate side-chains 155 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 167 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 31 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 121 THR 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 176 SER Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 209 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 58 optimal weight: 0.5980 chunk 70 optimal weight: 0.0970 chunk 14 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 50 optimal weight: 0.0870 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3549 r_free = 0.3549 target = 0.127340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099420 restraints weight = 9278.421| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.74 r_work: 0.3055 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6169 Z= 0.123 Angle : 0.670 9.394 8394 Z= 0.328 Chirality : 0.043 0.129 959 Planarity : 0.004 0.040 1047 Dihedral : 4.737 35.244 835 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 3.38 % Allowed : 33.04 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.31), residues: 772 helix: 1.54 (0.32), residues: 260 sheet: -0.48 (0.38), residues: 202 loop : -1.19 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 159 HIS 0.002 0.000 HIS B 17 PHE 0.011 0.001 PHE L 118 TYR 0.010 0.001 TYR A 146 ARG 0.005 0.000 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 279) hydrogen bonds : angle 4.26077 ( 846) SS BOND : bond 0.00442 ( 4) SS BOND : angle 1.80706 ( 8) covalent geometry : bond 0.00279 ( 6165) covalent geometry : angle 0.66815 ( 8386) ********************** 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 160 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.734 Fit side-chains REVERT: A 55 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8439 (mp) REVERT: A 96 CYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8186 (m) REVERT: A 180 ARG cc_start: 0.6704 (mtt-85) cc_final: 0.6306 (mmt-90) REVERT: A 182 GLN cc_start: 0.7331 (pm20) cc_final: 0.6550 (pt0) REVERT: A 183 TYR cc_start: 0.6840 (m-80) cc_final: 0.6450 (m-80) REVERT: B 29 ASN cc_start: 0.8293 (p0) cc_final: 0.8043 (p0) REVERT: H 73 ASP cc_start: 0.8587 (t0) cc_final: 0.8305 (t0) REVERT: L 9 SER cc_start: 0.8623 (OUTLIER) cc_final: 0.8348 (m) REVERT: L 79 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8339 (mp0) REVERT: L 209 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7229 (t80) outliers start: 23 outliers final: 17 residues processed: 154 average time/residue: 0.9565 time to fit residues: 157.3057 Evaluate side-chains 151 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 167 LEU 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 121 THR 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 9 SER 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 209 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 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 209 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.098024 restraints weight = 9375.060| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.73 r_work: 0.3034 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1840 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= 0.146 Angle : 0.677 9.529 8394 Z= 0.331 Chirality : 0.044 0.142 959 Planarity : 0.004 0.040 1047 Dihedral : 4.820 36.820 835 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.38 % Allowed : 32.75 % Favored : 63.88 % 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 (0.31), residues: 772 helix: 1.49 (0.32), residues: 260 sheet: -0.49 (0.38), residues: 202 loop : -1.21 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 159 HIS 0.001 0.000 HIS B 17 PHE 0.010 0.001 PHE L 118 TYR 0.010 0.001 TYR A 146 ARG 0.007 0.000 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 279) hydrogen bonds : angle 4.25331 ( 846) SS BOND : bond 0.00481 ( 4) SS BOND : angle 2.08076 ( 8) covalent geometry : bond 0.00342 ( 6165) covalent geometry : angle 0.67380 ( 8386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5126.83 seconds wall clock time: 90 minutes 14.04 seconds (5414.04 seconds total)