Starting phenix.real_space_refine on Thu Mar 6 05:13:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aza_15757/03_2025/8aza_15757.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aza_15757/03_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_15757/03_2025/8aza_15757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aza_15757/03_2025/8aza_15757.map" model { file = "/net/cci-nas-00/data/ceres_data/8aza_15757/03_2025/8aza_15757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aza_15757/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.51, per 1000 atoms: 0.71 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: 1.19 Conformation dependent library (CDL) restraints added in 581.5 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: 0.47 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: 1.10 Time building geometry restraints manager: 1.44 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: 2.400 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.810 Find NCS groups from input model: 0.130 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.350 ------------------------------------------------------------------------------- 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 : 0.520 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: 0.1700 time to fit residues: 17.5215 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 : 0.458 ------------------------------------------------------------------------------- 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 = 55)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.093750 restraints weight = 20874.912| |-----------------------------------------------------------------------------| 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 : 0.539 Fit side-chains revert: symmetry clash REVERT: C 209 ASN cc_start: 0.4807 (OUTLIER) cc_final: 0.3951 (m-40) REVERT: A 193 MET cc_start: 0.8100 (ppp) cc_final: 0.7515 (ppp) REVERT: A 276 ASN cc_start: 0.8464 (p0) cc_final: 0.8229 (p0) REVERT: B 98 MET cc_start: 0.1678 (ptp) cc_final: 0.1270 (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: 0.1498 time to fit residues: 19.4098 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 : 0.462 ------------------------------------------------------------------------------- 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: 2.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.114777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.093415 restraints weight = 20886.236| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 7.44 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5102 Z= 0.248 Angle : 0.683 10.020 6921 Z= 0.330 Chirality : 0.045 0.201 759 Planarity : 0.005 0.056 877 Dihedral : 4.880 47.584 664 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.95 % Allowed : 30.28 % 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: -0.49 (0.35), residues: 588 helix: 0.28 (0.34), residues: 246 sheet: -2.68 (0.62), residues: 57 loop : -0.19 (0.37), residues: 285 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 0.011 0.001 TYR B 215 ARG 0.003 0.000 ARG B 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 101 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8241 (ppp) cc_final: 0.7761 (ppp) REVERT: B 98 MET cc_start: 0.2232 (ptp) cc_final: 0.1722 (ptp) REVERT: B 265 MET cc_start: 0.8531 (mmt) cc_final: 0.8023 (mmt) outliers start: 27 outliers final: 14 residues processed: 94 average time/residue: 0.1537 time to fit residues: 19.9765 Evaluate side-chains 80 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 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 B residue 21 LEU 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 Chi-restraints excluded: chain B residue 306 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.115369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.094028 restraints weight = 21455.634| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 7.60 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5102 Z= 0.213 Angle : 0.674 10.383 6921 Z= 0.320 Chirality : 0.044 0.154 759 Planarity : 0.005 0.055 877 Dihedral : 4.784 46.869 664 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 6.79 % Allowed : 28.99 % Favored : 64.22 % 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: -0.42 (0.35), residues: 588 helix: 0.33 (0.34), residues: 246 sheet: -2.57 (0.64), residues: 57 loop : -0.16 (0.37), residues: 285 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 0.013 0.001 PHE A 229 TYR 0.013 0.001 TYR C 191 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 113 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 76 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.7287 (pt) cc_final: 0.7075 (mt) REVERT: A 193 MET cc_start: 0.8175 (ppp) cc_final: 0.7810 (ppp) REVERT: A 275 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8152 (mm-40) REVERT: A 276 ASN cc_start: 0.8613 (p0) cc_final: 0.8369 (p0) REVERT: B 98 MET cc_start: 0.2362 (OUTLIER) cc_final: 0.2085 (ptp) REVERT: B 265 MET cc_start: 0.8555 (mmt) cc_final: 0.7994 (mmt) outliers start: 37 outliers final: 18 residues processed: 103 average time/residue: 0.1435 time to fit residues: 19.8425 Evaluate side-chains 88 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 46 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 56 LEU 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 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 116 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 261 HIS 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: 0.8980 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 3 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 6 optimal weight: 0.0060 chunk 45 optimal weight: 0.7980 overall best weight: 1.0198 ------------------------------------------------------------------------------- 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 ** 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 = 0.4466 r_free = 0.4466 target = 0.114772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.092585 restraints weight = 20401.417| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 8.03 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5102 Z= 0.228 Angle : 0.690 10.436 6921 Z= 0.328 Chirality : 0.045 0.156 759 Planarity : 0.005 0.055 877 Dihedral : 4.782 45.386 664 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 5.87 % Allowed : 29.36 % 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: -0.42 (0.35), residues: 588 helix: 0.35 (0.34), residues: 247 sheet: -2.49 (0.66), residues: 57 loop : -0.20 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 220 HIS 0.005 0.001 HIS B 159 PHE 0.012 0.001 PHE A 229 TYR 0.013 0.001 TYR C 191 ARG 0.004 0.000 ARG A 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 105 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6554 (mttt) REVERT: A 220 TRP cc_start: 0.7192 (OUTLIER) cc_final: 0.6685 (t60) REVERT: A 275 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7743 (mm110) REVERT: A 276 ASN cc_start: 0.8694 (p0) cc_final: 0.8413 (p0) REVERT: B 98 MET cc_start: 0.2478 (OUTLIER) cc_final: 0.2079 (ptp) REVERT: B 265 MET cc_start: 0.8521 (mmt) cc_final: 0.7886 (mmt) outliers start: 32 outliers final: 17 residues processed: 95 average time/residue: 0.1893 time to fit residues: 25.4447 Evaluate side-chains 89 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 161 LYS 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 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 139 THR 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: 10.0000 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 21 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4505 r_free = 0.4505 target = 0.115948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.093751 restraints weight = 20715.332| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 7.87 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5102 Z= 0.201 Angle : 0.698 11.218 6921 Z= 0.328 Chirality : 0.046 0.225 759 Planarity : 0.005 0.052 877 Dihedral : 4.703 45.979 664 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.22 % Allowed : 30.46 % Favored : 65.32 % 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: -0.34 (0.35), residues: 588 helix: 0.43 (0.35), residues: 234 sheet: -2.35 (0.67), residues: 57 loop : -0.18 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 220 HIS 0.003 0.001 HIS B 159 PHE 0.013 0.001 PHE A 229 TYR 0.015 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 97 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.7455 (pt) cc_final: 0.7205 (tp) REVERT: A 220 TRP cc_start: 0.7236 (OUTLIER) cc_final: 0.6816 (t60) REVERT: A 276 ASN cc_start: 0.8849 (p0) cc_final: 0.8633 (p0) REVERT: B 98 MET cc_start: 0.2385 (OUTLIER) cc_final: 0.1855 (ptp) REVERT: B 265 MET cc_start: 0.8570 (mmt) cc_final: 0.8002 (mmt) outliers start: 23 outliers final: 14 residues processed: 91 average time/residue: 0.2177 time to fit residues: 27.1655 Evaluate side-chains 85 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 108 HIS ** 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 = 0.4447 r_free = 0.4447 target = 0.111900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.091437 restraints weight = 20838.607| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 7.43 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3411 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= 0.267 Angle : 0.755 15.501 6921 Z= 0.355 Chirality : 0.047 0.220 759 Planarity : 0.005 0.050 877 Dihedral : 4.760 43.918 664 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.14 % Allowed : 28.99 % Favored : 65.87 % 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: 0.22 (0.34), residues: 241 sheet: -2.31 (0.68), residues: 56 loop : -0.22 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 220 HIS 0.003 0.001 HIS B 261 PHE 0.012 0.001 PHE A 229 TYR 0.018 0.002 TYR B 134 ARG 0.007 0.000 ARG B 225 *********************** 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 99 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 TRP cc_start: 0.7319 (OUTLIER) cc_final: 0.6752 (t60) REVERT: A 275 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8300 (mm-40) REVERT: A 276 ASN cc_start: 0.8967 (p0) cc_final: 0.8730 (p0) REVERT: B 98 MET cc_start: 0.1940 (OUTLIER) cc_final: 0.1668 (ptp) REVERT: B 146 ASP cc_start: 0.8119 (t0) cc_final: 0.7531 (t0) REVERT: B 265 MET cc_start: 0.8612 (mmt) cc_final: 0.8071 (mmm) outliers start: 28 outliers final: 19 residues processed: 89 average time/residue: 0.2007 time to fit residues: 24.6513 Evaluate side-chains 89 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 56 LEU 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 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 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 139 THR 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: 1.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.112312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.092412 restraints weight = 21237.278| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 7.25 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3624 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= 0.245 Angle : 0.755 16.166 6921 Z= 0.349 Chirality : 0.047 0.215 759 Planarity : 0.005 0.050 877 Dihedral : 4.737 43.903 664 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.77 % Allowed : 29.72 % 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: -0.48 (0.35), residues: 588 helix: 0.28 (0.35), residues: 235 sheet: -2.32 (0.69), residues: 56 loop : -0.26 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 220 HIS 0.006 0.001 HIS B 159 PHE 0.017 0.001 PHE A 229 TYR 0.016 0.001 TYR B 134 ARG 0.005 0.000 ARG B 225 *********************** 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 92 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 TRP cc_start: 0.7333 (OUTLIER) cc_final: 0.6684 (t60) REVERT: A 275 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8274 (mm-40) REVERT: A 276 ASN cc_start: 0.8971 (p0) cc_final: 0.8751 (p0) REVERT: B 98 MET cc_start: 0.2089 (OUTLIER) cc_final: 0.1394 (ptp) REVERT: B 146 ASP cc_start: 0.7891 (t0) cc_final: 0.7411 (t0) REVERT: B 265 MET cc_start: 0.8609 (mmt) cc_final: 0.8053 (mmm) outliers start: 26 outliers final: 18 residues processed: 84 average time/residue: 0.2587 time to fit residues: 32.2524 Evaluate side-chains 87 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 56 LEU 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 A residue 220 TRP Chi-restraints excluded: chain A residue 254 SER 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 116 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 139 THR 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: 2.9990 chunk 29 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** 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 = 0.4445 r_free = 0.4445 target = 0.111296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.091600 restraints weight = 20806.468| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 7.16 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4059 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= 0.252 Angle : 0.764 16.573 6921 Z= 0.353 Chirality : 0.047 0.218 759 Planarity : 0.005 0.054 877 Dihedral : 4.745 42.490 664 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.59 % Allowed : 29.72 % Favored : 65.69 % 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: 0.22 (0.35), residues: 235 sheet: -2.42 (0.62), residues: 66 loop : -0.24 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 220 HIS 0.010 0.001 HIS B 159 PHE 0.015 0.001 PHE A 229 TYR 0.017 0.002 TYR B 134 ARG 0.005 0.000 ARG B 225 *********************** 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 91 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.7873 (mm-40) REVERT: A 276 ASN cc_start: 0.9084 (p0) cc_final: 0.8810 (p0) REVERT: B 98 MET cc_start: 0.2363 (OUTLIER) cc_final: 0.2034 (ptp) REVERT: B 146 ASP cc_start: 0.7890 (t0) cc_final: 0.7472 (t0) REVERT: B 265 MET cc_start: 0.8652 (mmt) cc_final: 0.7935 (mmt) outliers start: 25 outliers final: 18 residues processed: 83 average time/residue: 0.1637 time to fit residues: 19.8840 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 : 0.713 ------------------------------------------------------------------------------- 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 56 LEU 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 254 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 30 optimal weight: 0.0970 chunk 27 optimal weight: 0.4980 chunk 37 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 0.0370 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** 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 = 0.4484 r_free = 0.4484 target = 0.113786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.094191 restraints weight = 21063.322| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 7.46 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4094 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= 0.216 Angle : 0.781 17.074 6921 Z= 0.360 Chirality : 0.046 0.206 759 Planarity : 0.005 0.057 877 Dihedral : 4.314 16.738 662 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.67 % Allowed : 31.56 % 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: -0.61 (0.34), residues: 588 helix: 0.23 (0.34), residues: 235 sheet: -2.40 (0.62), residues: 67 loop : -0.28 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 220 HIS 0.006 0.001 HIS B 159 PHE 0.019 0.001 PHE A 229 TYR 0.019 0.001 TYR B 134 ARG 0.005 0.000 ARG B 225 ********************** 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 89 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ASN cc_start: 0.8979 (p0) cc_final: 0.8761 (p0) REVERT: B 98 MET cc_start: 0.2168 (OUTLIER) cc_final: 0.1629 (ptp) REVERT: B 146 ASP cc_start: 0.7778 (t0) cc_final: 0.7355 (t0) REVERT: B 265 MET cc_start: 0.8589 (mmt) cc_final: 0.8040 (mmm) outliers start: 20 outliers final: 16 residues processed: 80 average time/residue: 0.1519 time to fit residues: 17.2474 Evaluate side-chains 84 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 254 SER 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 108 HIS Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 261 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 chunk 29 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 0.0670 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 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 = 0.4500 r_free = 0.4500 target = 0.114741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.095129 restraints weight = 21189.626| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 7.38 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5102 Z= 0.209 Angle : 0.761 17.136 6921 Z= 0.351 Chirality : 0.046 0.203 759 Planarity : 0.005 0.056 877 Dihedral : 4.231 16.228 662 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.49 % Allowed : 31.74 % 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: -0.57 (0.34), residues: 588 helix: 0.30 (0.34), residues: 234 sheet: -2.37 (0.61), residues: 67 loop : -0.30 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 220 HIS 0.006 0.001 HIS B 159 PHE 0.019 0.001 PHE A 229 TYR 0.018 0.001 TYR B 134 ARG 0.004 0.000 ARG B 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3368.89 seconds wall clock time: 62 minutes 14.66 seconds (3734.66 seconds total)