Starting phenix.real_space_refine on Tue Feb 11 09:14:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aza_15757/02_2025/8aza_15757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aza_15757/02_2025/8aza_15757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aza_15757/02_2025/8aza_15757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aza_15757/02_2025/8aza_15757.map" model { file = "/net/cci-nas-00/data/ceres_data/8aza_15757/02_2025/8aza_15757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aza_15757/02_2025/8aza_15757.cif" } resolution = 3.15 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= -0.001 sd= 0.025 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 20 5.16 5 C 3204 2.51 5 N 872 2.21 5 O 873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4970 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 624 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "A" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2327 Classifications: {'peptide': 284} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 263} Chain breaks: 3 Chain: "B" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 2018 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 229} Chain breaks: 3 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 336 SG CYS C 200 35.671 18.583 82.528 1.00273.60 S ATOM 359 SG CYS C 203 39.057 18.926 84.298 1.00305.23 S ATOM 564 SG CYS C 227 38.823 16.632 81.459 1.00267.04 S Time building chain proxies: 3.85, per 1000 atoms: 0.77 Number of scatterers: 4970 At special positions: 0 Unit cell: (71.949, 76.911, 95.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 20 16.00 O 873 8.00 N 872 7.00 C 3204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.26 Conformation dependent library (CDL) restraints added in 586.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 220 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 227 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 203 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 200 " Number of angles added : 3 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 8 sheets defined 43.9% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'C' and resid 162 through 170 removed outlier: 3.570A pdb=" N ARG C 166 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 188 Processing helix chain 'C' and resid 215 through 224 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'A' and resid 56 through 73 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 117 through 136 removed outlier: 3.989A pdb=" N LEU A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 4.012A pdb=" N MET A 193 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 225 removed outlier: 4.066A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 223 " --> pdb=" O THR A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 removed outlier: 4.093A pdb=" N MET A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 273 Processing helix chain 'A' and resid 282 through 295 Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 298 through 313 removed outlier: 3.847A pdb=" N ILE A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 16 No H-bonds generated for 'chain 'B' and resid 14 through 16' Processing helix chain 'B' and resid 60 through 73 Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.718A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 136 Processing helix chain 'B' and resid 164 through 168 removed outlier: 4.541A pdb=" N LEU B 167 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 225 Processing helix chain 'B' and resid 261 through 273 Processing helix chain 'B' and resid 282 through 297 Proline residue: B 292 - end of helix removed outlier: 3.843A pdb=" N PHE B 297 " --> pdb=" O VAL B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 314 removed outlier: 3.625A pdb=" N PHE B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 189 through 191 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 23 removed outlier: 4.777A pdb=" N ASP A 20 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 36 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY A 92 " --> pdb=" O CYS A 85 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 85 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU A 96 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE A 81 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 143 removed outlier: 3.719A pdb=" N LEU A 143 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 26 removed outlier: 4.589A pdb=" N LEU B 21 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER B 34 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR B 23 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N VAL B 32 " --> pdb=" O TYR B 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.639A pdb=" N GLY B 83 " --> pdb=" O VAL B 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 142 through 143 removed outlier: 3.825A pdb=" N LEU B 143 " --> pdb=" O LYS B 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 154 197 hydrogen bonds defined for protein. 564 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: 1.28 Time building geometry restraints manager: 1.46 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: 1581 1.34 - 1.46: 816 1.46 - 1.58: 2673 1.58 - 1.70: 1 1.70 - 1.82: 31 Bond restraints: 5102 Sorted by residual: bond pdb=" CB PRO C 181 " pdb=" CG PRO C 181 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.89e+00 bond pdb=" CA LEU A 309 " pdb=" C LEU A 309 " ideal model delta sigma weight residual 1.524 1.502 0.021 1.32e-02 5.74e+03 2.61e+00 bond pdb=" C LEU A 309 " pdb=" O LEU A 309 " ideal model delta sigma weight residual 1.236 1.217 0.019 1.22e-02 6.72e+03 2.38e+00 bond pdb=" CG PRO C 181 " pdb=" CD PRO C 181 " ideal model delta sigma weight residual 1.503 1.551 -0.048 3.40e-02 8.65e+02 1.98e+00 bond pdb=" CB LYS B 61 " pdb=" CG LYS B 61 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.96e+00 ... (remaining 5097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 6727 1.93 - 3.87: 148 3.87 - 5.80: 27 5.80 - 7.74: 13 7.74 - 9.67: 6 Bond angle restraints: 6921 Sorted by residual: angle pdb=" N ASP A 278 " pdb=" CA ASP A 278 " pdb=" C ASP A 278 " ideal model delta sigma weight residual 111.28 117.77 -6.49 1.09e+00 8.42e-01 3.54e+01 angle pdb=" C ASN A 276 " pdb=" N PRO A 277 " pdb=" CA PRO A 277 " ideal model delta sigma weight residual 119.87 124.81 -4.94 1.04e+00 9.25e-01 2.26e+01 angle pdb=" N PRO A 277 " pdb=" CA PRO A 277 " pdb=" C PRO A 277 " ideal model delta sigma weight residual 114.03 119.01 -4.98 1.23e+00 6.61e-01 1.64e+01 angle pdb=" CA PRO C 181 " pdb=" N PRO C 181 " pdb=" CD PRO C 181 " ideal model delta sigma weight residual 112.00 106.47 5.53 1.40e+00 5.10e-01 1.56e+01 angle pdb=" CA LYS B 61 " pdb=" CB LYS B 61 " pdb=" CG LYS B 61 " ideal model delta sigma weight residual 114.10 121.79 -7.69 2.00e+00 2.50e-01 1.48e+01 ... (remaining 6916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2606 17.94 - 35.87: 339 35.87 - 53.81: 101 53.81 - 71.74: 20 71.74 - 89.68: 7 Dihedral angle restraints: 3073 sinusoidal: 1286 harmonic: 1787 Sorted by residual: dihedral pdb=" C ASP A 278 " pdb=" N ASP A 278 " pdb=" CA ASP A 278 " pdb=" CB ASP A 278 " ideal model delta harmonic sigma weight residual -122.60 -133.29 10.69 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" N ASP A 278 " pdb=" C ASP A 278 " pdb=" CA ASP A 278 " pdb=" CB ASP A 278 " ideal model delta harmonic sigma weight residual 122.80 133.27 -10.47 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" CA MET A 98 " pdb=" C MET A 98 " pdb=" N PRO A 99 " pdb=" CA PRO A 99 " ideal model delta harmonic sigma weight residual 180.00 -163.14 -16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 3070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 697 0.085 - 0.170: 58 0.170 - 0.254: 2 0.254 - 0.339: 1 0.339 - 0.424: 1 Chirality restraints: 759 Sorted by residual: chirality pdb=" CA ASP A 278 " pdb=" N ASP A 278 " pdb=" C ASP A 278 " pdb=" CB ASP A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" CB VAL B 222 " pdb=" CA VAL B 222 " pdb=" CG1 VAL B 222 " pdb=" CG2 VAL B 222 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA GLU A 279 " pdb=" N GLU A 279 " pdb=" C GLU A 279 " pdb=" CB GLU A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 756 not shown) Planarity restraints: 877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 280 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO B 281 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO B 281 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 281 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 180 " 0.063 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO C 181 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 308 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C GLN A 308 " -0.040 2.00e-02 2.50e+03 pdb=" O GLN A 308 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 309 " 0.013 2.00e-02 2.50e+03 ... (remaining 874 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 525 2.74 - 3.28: 5526 3.28 - 3.82: 9009 3.82 - 4.36: 10348 4.36 - 4.90: 16487 Nonbonded interactions: 41895 Sorted by model distance: nonbonded pdb=" O VAL B 293 " pdb=" OG1 THR B 296 " model vdw 2.202 3.040 nonbonded pdb=" OE1 GLU A 196 " pdb=" OG SER A 207 " model vdw 2.238 3.040 nonbonded pdb=" O ASN A 234 " pdb=" NE2 GLN A 237 " model vdw 2.280 3.120 nonbonded pdb=" NH2 ARG A 247 " pdb=" O TRP A 273 " model vdw 2.303 3.120 nonbonded pdb=" NE2 HIS A 136 " pdb=" OD2 ASP A 211 " model vdw 2.308 3.120 ... (remaining 41890 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 49 or resid 59 through 171 or resid 206 through \ 228 or resid 247 through 314)) selection = chain 'B' } 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=0.00 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.780 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 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 : 0.004 0.085 5102 Z= 0.249 Angle : 0.758 9.671 6921 Z= 0.386 Chirality : 0.049 0.424 759 Planarity : 0.006 0.104 877 Dihedral : 17.832 89.676 1907 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 26.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.73 % Allowed : 33.39 % Favored : 65.87 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 5.00 % 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: -0.75 (0.34), residues: 588 helix: -0.08 (0.33), residues: 247 sheet: -2.64 (0.61), residues: 63 loop : -0.15 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 220 HIS 0.004 0.001 HIS B 144 PHE 0.014 0.001 PHE A 229 TYR 0.013 0.001 TYR B 134 ARG 0.002 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8022 (ppp) cc_final: 0.7004 (ppp) REVERT: B 61 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8807 (tppt) outliers start: 4 outliers final: 4 residues processed: 80 average time/residue: 0.1722 time to fit residues: 18.0388 Evaluate side-chains 72 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 223 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 15 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN A 136 HIS ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN B 108 HIS B 227 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.116782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.093746 restraints weight = 20874.918| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 8.08 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5102 Z= 0.252 Angle : 0.691 11.904 6921 Z= 0.336 Chirality : 0.045 0.157 759 Planarity : 0.005 0.071 877 Dihedral : 5.378 49.058 670 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.14 % Allowed : 29.36 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.71 (0.34), residues: 588 helix: 0.05 (0.33), residues: 254 sheet: -2.88 (0.57), residues: 65 loop : -0.15 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 118 HIS 0.004 0.001 HIS A 261 PHE 0.012 0.001 PHE A 229 TYR 0.020 0.002 TYR C 191 ARG 0.004 0.001 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: C 209 ASN cc_start: 0.4809 (OUTLIER) cc_final: 0.3952 (m-40) REVERT: A 193 MET cc_start: 0.8101 (ppp) cc_final: 0.7515 (ppp) REVERT: A 276 ASN cc_start: 0.8464 (p0) cc_final: 0.8228 (p0) REVERT: B 98 MET cc_start: 0.1679 (ptp) cc_final: 0.1269 (ptp) REVERT: B 265 MET cc_start: 0.8533 (mmt) cc_final: 0.8119 (mmt) outliers start: 28 outliers final: 14 residues processed: 95 average time/residue: 0.1463 time to fit residues: 19.1154 Evaluate side-chains 82 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 26 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.0770 chunk 39 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.118049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.094417 restraints weight = 20731.900| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 8.65 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5102 Z= 0.199 Angle : 0.663 9.997 6921 Z= 0.317 Chirality : 0.044 0.188 759 Planarity : 0.005 0.056 877 Dihedral : 4.834 49.590 664 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.22 % Allowed : 30.64 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.50 (0.34), residues: 588 helix: 0.24 (0.33), residues: 252 sheet: -2.65 (0.62), residues: 57 loop : -0.18 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 118 HIS 0.003 0.001 HIS A 136 PHE 0.012 0.001 PHE A 229 TYR 0.011 0.001 TYR B 134 ARG 0.003 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8110 (ppp) cc_final: 0.7658 (ppp) REVERT: A 270 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8928 (mm-30) REVERT: B 98 MET cc_start: 0.2143 (ptp) cc_final: 0.1526 (ptp) REVERT: B 265 MET cc_start: 0.8504 (mmt) cc_final: 0.8008 (mmt) outliers start: 23 outliers final: 13 residues processed: 89 average time/residue: 0.1443 time to fit residues: 17.5483 Evaluate side-chains 79 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 43 optimal weight: 0.0770 chunk 4 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN A 71 HIS ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.116658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.095613 restraints weight = 20410.454| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 7.47 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5102 Z= 0.203 Angle : 0.661 9.977 6921 Z= 0.313 Chirality : 0.044 0.156 759 Planarity : 0.005 0.054 877 Dihedral : 4.783 48.103 664 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.69 % Allowed : 28.26 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.33 (0.34), residues: 588 helix: 0.48 (0.34), residues: 240 sheet: -2.55 (0.63), residues: 57 loop : -0.17 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 118 HIS 0.004 0.001 HIS A 136 PHE 0.012 0.001 PHE A 229 TYR 0.015 0.001 TYR B 134 ARG 0.003 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 193 MET cc_start: 0.8077 (ppp) cc_final: 0.7732 (ppp) REVERT: A 276 ASN cc_start: 0.8550 (p0) cc_final: 0.8322 (p0) REVERT: B 98 MET cc_start: 0.2222 (OUTLIER) cc_final: 0.1873 (ptp) REVERT: B 265 MET cc_start: 0.8531 (mmt) cc_final: 0.7966 (mmt) outliers start: 31 outliers final: 14 residues processed: 99 average time/residue: 0.1486 time to fit residues: 19.7827 Evaluate side-chains 83 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 57 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN ** B 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.109138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.088621 restraints weight = 20597.034| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 7.14 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 5102 Z= 0.389 Angle : 0.801 10.673 6921 Z= 0.390 Chirality : 0.048 0.195 759 Planarity : 0.006 0.055 877 Dihedral : 5.134 42.937 664 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 30.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 6.42 % Allowed : 28.62 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.89 (0.35), residues: 588 helix: -0.00 (0.33), residues: 253 sheet: -2.80 (0.56), residues: 74 loop : -0.28 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 118 HIS 0.007 0.002 HIS B 261 PHE 0.013 0.002 PHE A 229 TYR 0.018 0.002 TYR C 191 ARG 0.005 0.001 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 71 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7432 (pt) REVERT: A 220 TRP cc_start: 0.7372 (OUTLIER) cc_final: 0.6930 (t60) REVERT: A 275 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8351 (mm-40) REVERT: A 276 ASN cc_start: 0.9068 (p0) cc_final: 0.8835 (p0) REVERT: B 98 MET cc_start: 0.2363 (OUTLIER) cc_final: 0.2100 (ptp) REVERT: B 265 MET cc_start: 0.8751 (mmt) cc_final: 0.8099 (mmt) outliers start: 35 outliers final: 17 residues processed: 97 average time/residue: 0.1316 time to fit residues: 17.7220 Evaluate side-chains 85 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 24 optimal weight: 0.0670 chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.113924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.092050 restraints weight = 20164.420| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 7.68 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5102 Z= 0.217 Angle : 0.724 10.905 6921 Z= 0.341 Chirality : 0.047 0.253 759 Planarity : 0.005 0.052 877 Dihedral : 4.935 44.870 664 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.59 % Allowed : 30.83 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.35), residues: 588 helix: 0.20 (0.34), residues: 247 sheet: -2.55 (0.65), residues: 56 loop : -0.27 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 220 HIS 0.004 0.001 HIS B 159 PHE 0.011 0.001 PHE A 229 TYR 0.014 0.001 TYR B 134 ARG 0.003 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8367 (mm-40) REVERT: A 276 ASN cc_start: 0.9015 (p0) cc_final: 0.8812 (p0) REVERT: B 98 MET cc_start: 0.2379 (OUTLIER) cc_final: 0.1945 (ptp) REVERT: B 265 MET cc_start: 0.8637 (mmt) cc_final: 0.8062 (mmt) outliers start: 25 outliers final: 16 residues processed: 85 average time/residue: 0.1536 time to fit residues: 17.7791 Evaluate side-chains 85 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.112585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.091093 restraints weight = 20276.815| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 7.73 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5102 Z= 0.243 Angle : 0.735 15.579 6921 Z= 0.348 Chirality : 0.047 0.218 759 Planarity : 0.005 0.051 877 Dihedral : 4.838 43.687 664 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.14 % Allowed : 30.09 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.54 (0.35), residues: 588 helix: 0.20 (0.34), residues: 247 sheet: -2.59 (0.65), residues: 57 loop : -0.21 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 118 HIS 0.003 0.001 HIS B 159 PHE 0.013 0.001 PHE A 229 TYR 0.016 0.002 TYR B 134 ARG 0.004 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.1716 (OUTLIER) cc_final: 0.1480 (mt-10) REVERT: A 220 TRP cc_start: 0.7359 (OUTLIER) cc_final: 0.6693 (t60) REVERT: A 275 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8428 (mm-40) REVERT: A 276 ASN cc_start: 0.9044 (p0) cc_final: 0.8789 (p0) REVERT: B 98 MET cc_start: 0.2390 (OUTLIER) cc_final: 0.1625 (ptp) REVERT: B 146 ASP cc_start: 0.7790 (t0) cc_final: 0.7572 (p0) REVERT: B 265 MET cc_start: 0.8596 (mmt) cc_final: 0.8048 (mmm) outliers start: 28 outliers final: 18 residues processed: 85 average time/residue: 0.1440 time to fit residues: 16.9886 Evaluate side-chains 88 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 48 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.112073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.091996 restraints weight = 21382.885| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 7.48 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5102 Z= 0.238 Angle : 0.735 16.156 6921 Z= 0.345 Chirality : 0.046 0.225 759 Planarity : 0.005 0.050 877 Dihedral : 4.812 43.353 664 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.14 % Allowed : 29.91 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.49 (0.35), residues: 588 helix: 0.26 (0.35), residues: 241 sheet: -2.42 (0.67), residues: 56 loop : -0.24 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 220 HIS 0.007 0.001 HIS B 159 PHE 0.015 0.001 PHE A 229 TYR 0.017 0.001 TYR B 134 ARG 0.004 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.7827 (mt) cc_final: 0.7480 (pt) REVERT: A 220 TRP cc_start: 0.7340 (OUTLIER) cc_final: 0.6604 (t60) REVERT: A 275 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8323 (mm-40) REVERT: A 276 ASN cc_start: 0.9012 (p0) cc_final: 0.8772 (p0) REVERT: B 98 MET cc_start: 0.2093 (OUTLIER) cc_final: 0.1604 (ptp) REVERT: B 146 ASP cc_start: 0.7712 (t0) cc_final: 0.7028 (t0) REVERT: B 153 LEU cc_start: 0.8128 (tt) cc_final: 0.7819 (mm) REVERT: B 265 MET cc_start: 0.8621 (mmt) cc_final: 0.8065 (mmm) outliers start: 28 outliers final: 17 residues processed: 86 average time/residue: 0.1339 time to fit residues: 16.1094 Evaluate side-chains 85 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 220 TRP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 52 optimal weight: 0.0770 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.113832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.094105 restraints weight = 20760.356| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 7.30 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5102 Z= 0.217 Angle : 0.748 16.791 6921 Z= 0.352 Chirality : 0.046 0.219 759 Planarity : 0.005 0.049 877 Dihedral : 4.405 18.969 662 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.85 % Allowed : 31.01 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.49 (0.35), residues: 588 helix: 0.31 (0.35), residues: 235 sheet: -2.44 (0.65), residues: 58 loop : -0.25 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 220 HIS 0.009 0.001 HIS B 159 PHE 0.014 0.001 PHE A 229 TYR 0.015 0.001 TYR B 134 ARG 0.003 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.7844 (mt) cc_final: 0.7470 (pt) REVERT: A 275 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.7750 (mm-40) REVERT: A 276 ASN cc_start: 0.8950 (p0) cc_final: 0.8727 (p0) REVERT: B 98 MET cc_start: 0.2222 (OUTLIER) cc_final: 0.2017 (ptp) REVERT: B 146 ASP cc_start: 0.7704 (t0) cc_final: 0.7399 (p0) REVERT: B 153 LEU cc_start: 0.8111 (tt) cc_final: 0.7810 (mm) REVERT: B 265 MET cc_start: 0.8568 (mmt) cc_final: 0.8017 (mmm) outliers start: 21 outliers final: 14 residues processed: 85 average time/residue: 0.1387 time to fit residues: 16.1514 Evaluate side-chains 83 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.111088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.091119 restraints weight = 21097.159| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 7.40 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5102 Z= 0.267 Angle : 0.779 17.205 6921 Z= 0.367 Chirality : 0.047 0.219 759 Planarity : 0.005 0.053 877 Dihedral : 4.480 19.951 662 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.67 % Allowed : 31.19 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.60 (0.35), residues: 588 helix: 0.25 (0.35), residues: 235 sheet: -2.49 (0.60), residues: 66 loop : -0.26 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 220 HIS 0.010 0.001 HIS B 159 PHE 0.018 0.001 PHE A 229 TYR 0.019 0.002 TYR A 77 ARG 0.005 0.000 ARG B 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1176 Ramachandran restraints generated. 588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.7781 (mt) cc_final: 0.7455 (pt) REVERT: A 275 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7909 (mm-40) REVERT: A 276 ASN cc_start: 0.9120 (p0) cc_final: 0.8870 (p0) REVERT: B 93 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7893 (mp) REVERT: B 98 MET cc_start: 0.2256 (OUTLIER) cc_final: 0.1525 (ptp) REVERT: B 146 ASP cc_start: 0.7627 (t0) cc_final: 0.7262 (t0) REVERT: B 153 LEU cc_start: 0.8098 (tt) cc_final: 0.7888 (tt) REVERT: B 265 MET cc_start: 0.8639 (mmt) cc_final: 0.7943 (mmt) outliers start: 20 outliers final: 14 residues processed: 78 average time/residue: 0.1368 time to fit residues: 15.0990 Evaluate side-chains 81 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 261 HIS Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.2980 chunk 29 optimal weight: 0.0670 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.113443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.093609 restraints weight = 21036.863| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 7.39 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5102 Z= 0.221 Angle : 0.761 17.125 6921 Z= 0.354 Chirality : 0.046 0.221 759 Planarity : 0.005 0.054 877 Dihedral : 4.391 20.760 662 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.85 % Allowed : 31.01 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.59 (0.35), residues: 588 helix: 0.13 (0.34), residues: 241 sheet: -2.35 (0.66), residues: 57 loop : -0.26 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 220 HIS 0.009 0.001 HIS B 159 PHE 0.018 0.001 PHE A 229 TYR 0.014 0.002 TYR B 134 ARG 0.003 0.000 ARG A 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2983.12 seconds wall clock time: 53 minutes 38.93 seconds (3218.93 seconds total)