Starting phenix.real_space_refine on Wed Mar 5 16:00:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vv6_32139/03_2025/7vv6_32139.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vv6_32139/03_2025/7vv6_32139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vv6_32139/03_2025/7vv6_32139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vv6_32139/03_2025/7vv6_32139.map" model { file = "/net/cci-nas-00/data/ceres_data/7vv6_32139/03_2025/7vv6_32139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vv6_32139/03_2025/7vv6_32139.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 1518 2.51 5 N 342 2.21 5 O 349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 2227 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2161 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'6IB': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.24, per 1000 atoms: 1.01 Number of scatterers: 2227 At special positions: 0 Unit cell: (65.224, 72.588, 61.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 349 8.00 N 342 7.00 C 1518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 258 " distance=2.04 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 272.3 milliseconds 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 508 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 84.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'R' and resid 30 through 57 removed outlier: 3.529A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 94 removed outlier: 3.831A pdb=" N VAL R 66 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 3.602A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 168 Processing helix chain 'R' and resid 176 through 212 removed outlier: 3.926A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 236 Processing helix chain 'R' and resid 236 through 245 removed outlier: 4.339A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 256 through 280 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 280 through 285 Processing helix chain 'R' and resid 286 through 288 No H-bonds generated for 'chain 'R' and resid 286 through 288' 169 hydrogen bonds defined for protein. 507 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.65 Time building geometry restraints manager: 0.79 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: 617 1.34 - 1.47: 662 1.47 - 1.59: 993 1.59 - 1.71: 1 1.71 - 1.84: 22 Bond restraints: 2295 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.669 -0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.335 1.368 -0.034 1.28e-02 6.10e+03 6.99e+00 bond pdb=" C31 6IB R 402 " pdb=" N5 6IB R 402 " ideal model delta sigma weight residual 1.447 1.496 -0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" C32 6IB R 402 " pdb=" N6 6IB R 402 " ideal model delta sigma weight residual 1.449 1.497 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" CB VAL R 131 " pdb=" CG2 VAL R 131 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.00e+00 ... (remaining 2290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 3010 3.21 - 6.43: 103 6.43 - 9.64: 14 9.64 - 12.86: 2 12.86 - 16.07: 2 Bond angle restraints: 3131 Sorted by residual: angle pdb=" N LEU R 237 " pdb=" CA LEU R 237 " pdb=" C LEU R 237 " ideal model delta sigma weight residual 113.45 120.88 -7.43 1.39e+00 5.18e-01 2.85e+01 angle pdb=" C TRP R 250 " pdb=" N LYS R 251 " pdb=" CA LYS R 251 " ideal model delta sigma weight residual 122.08 129.29 -7.21 1.47e+00 4.63e-01 2.41e+01 angle pdb=" C GLY R 236 " pdb=" N LEU R 237 " pdb=" CA LEU R 237 " ideal model delta sigma weight residual 120.58 127.01 -6.43 1.32e+00 5.74e-01 2.37e+01 angle pdb=" CA LEU R 226 " pdb=" CB LEU R 226 " pdb=" CG LEU R 226 " ideal model delta sigma weight residual 116.30 132.37 -16.07 3.50e+00 8.16e-02 2.11e+01 angle pdb=" N SER R 177 " pdb=" CA SER R 177 " pdb=" C SER R 177 " ideal model delta sigma weight residual 111.28 115.95 -4.67 1.09e+00 8.42e-01 1.83e+01 ... (remaining 3126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.72: 1034 12.72 - 25.44: 169 25.44 - 38.16: 97 38.16 - 50.88: 34 50.88 - 63.60: 21 Dihedral angle restraints: 1355 sinusoidal: 571 harmonic: 784 Sorted by residual: dihedral pdb=" CA THR R 30 " pdb=" C THR R 30 " pdb=" N LEU R 31 " pdb=" CA LEU R 31 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP R 254 " pdb=" C ASP R 254 " pdb=" N VAL R 255 " pdb=" CA VAL R 255 " ideal model delta harmonic sigma weight residual 180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ASP R 252 " pdb=" C ASP R 252 " pdb=" N SER R 253 " pdb=" CA SER R 253 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 1352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 253 0.061 - 0.122: 88 0.122 - 0.183: 23 0.183 - 0.244: 2 0.244 - 0.305: 2 Chirality restraints: 368 Sorted by residual: chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C9 CLR R 401 " pdb=" C10 CLR R 401 " pdb=" C11 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.70 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA LEU R 237 " pdb=" N LEU R 237 " pdb=" C LEU R 237 " pdb=" CB LEU R 237 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 365 not shown) Planarity restraints: 361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 149 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C VAL R 149 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL R 149 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS R 150 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 43 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C VAL R 43 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL R 43 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY R 44 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 40 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C ILE R 40 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE R 40 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA R 41 " -0.013 2.00e-02 2.50e+03 ... (remaining 358 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 629 2.81 - 3.33: 1941 3.33 - 3.86: 3854 3.86 - 4.38: 4171 4.38 - 4.90: 7427 Nonbonded interactions: 18022 Sorted by model distance: nonbonded pdb=" O GLY R 27 " pdb=" OH TYR R 89 " model vdw 2.291 3.040 nonbonded pdb=" O SER R 264 " pdb=" OG SER R 268 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.320 3.040 nonbonded pdb=" O SER R 98 " pdb=" OG SER R 98 " model vdw 2.322 3.040 nonbonded pdb=" O THR R 107 " pdb=" OG SER R 161 " model vdw 2.322 3.040 ... (remaining 18017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.270 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 : 0.010 0.134 2295 Z= 0.620 Angle : 1.380 16.073 3131 Z= 0.707 Chirality : 0.068 0.305 368 Planarity : 0.009 0.048 361 Dihedral : 19.052 63.599 841 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 10.37 % Allowed : 24.90 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.22 (0.34), residues: 269 helix: -2.49 (0.23), residues: 208 sheet: None (None), residues: 0 loop : -3.08 (0.63), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP R 289 HIS 0.004 0.001 HIS R 261 PHE 0.020 0.003 PHE R 183 TYR 0.021 0.004 TYR R 89 ARG 0.005 0.001 ARG R 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: R 109 MET cc_start: 0.8310 (ttp) cc_final: 0.7998 (ttm) REVERT: R 164 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7868 (tm-30) REVERT: R 166 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8433 (tptt) REVERT: R 201 SER cc_start: 0.9194 (m) cc_final: 0.8684 (p) REVERT: R 242 GLN cc_start: 0.8817 (pp30) cc_final: 0.8517 (pp30) outliers start: 25 outliers final: 1 residues processed: 67 average time/residue: 0.1188 time to fit residues: 9.6285 Evaluate side-chains 31 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 182 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.0020 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 HIS R 271 ASN R 275 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.109743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.082826 restraints weight = 3654.448| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.32 r_work: 0.2845 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2295 Z= 0.157 Angle : 0.634 9.071 3131 Z= 0.305 Chirality : 0.042 0.201 368 Planarity : 0.005 0.034 361 Dihedral : 10.409 56.949 380 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.90 % Allowed : 27.80 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.49), residues: 269 helix: 0.57 (0.33), residues: 218 sheet: None (None), residues: 0 loop : -2.01 (0.80), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 248 HIS 0.004 0.001 HIS R 144 PHE 0.013 0.001 PHE R 81 TYR 0.012 0.001 TYR R 222 ARG 0.007 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: R 109 MET cc_start: 0.8879 (ttp) cc_final: 0.8595 (ttm) REVERT: R 163 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8456 (tt) REVERT: R 166 LYS cc_start: 0.8917 (ttpp) cc_final: 0.8250 (tptt) outliers start: 7 outliers final: 2 residues processed: 41 average time/residue: 0.1477 time to fit residues: 7.2452 Evaluate side-chains 32 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.107861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.082590 restraints weight = 3797.950| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.17 r_work: 0.2853 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2295 Z= 0.171 Angle : 0.578 6.074 3131 Z= 0.279 Chirality : 0.041 0.147 368 Planarity : 0.004 0.031 361 Dihedral : 9.013 57.157 379 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.07 % Allowed : 26.97 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.52), residues: 269 helix: 1.62 (0.35), residues: 223 sheet: None (None), residues: 0 loop : -2.00 (0.81), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.008 0.001 PHE R 183 TYR 0.008 0.001 TYR R 222 ARG 0.002 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.230 Fit side-chains REVERT: R 109 MET cc_start: 0.8832 (ttp) cc_final: 0.8569 (ttm) REVERT: R 166 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8373 (tptt) REVERT: R 201 SER cc_start: 0.9333 (m) cc_final: 0.8969 (p) REVERT: R 242 GLN cc_start: 0.9152 (pp30) cc_final: 0.8885 (pp30) outliers start: 5 outliers final: 4 residues processed: 37 average time/residue: 0.1247 time to fit residues: 5.7158 Evaluate side-chains 38 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.0170 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.081371 restraints weight = 3677.436| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.27 r_work: 0.2824 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2295 Z= 0.158 Angle : 0.545 6.008 3131 Z= 0.267 Chirality : 0.040 0.157 368 Planarity : 0.003 0.029 361 Dihedral : 8.805 55.821 379 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.32 % Allowed : 25.73 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.53), residues: 269 helix: 2.06 (0.36), residues: 223 sheet: None (None), residues: 0 loop : -1.93 (0.82), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.006 0.001 PHE R 64 TYR 0.006 0.001 TYR R 113 ARG 0.002 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.222 Fit side-chains REVERT: R 38 LEU cc_start: 0.8900 (tp) cc_final: 0.8608 (tp) REVERT: R 75 ASP cc_start: 0.8867 (m-30) cc_final: 0.8493 (t0) REVERT: R 109 MET cc_start: 0.8871 (ttp) cc_final: 0.8542 (ttm) REVERT: R 163 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8350 (tt) REVERT: R 166 LYS cc_start: 0.8931 (ttpp) cc_final: 0.8318 (tptt) REVERT: R 201 SER cc_start: 0.9186 (m) cc_final: 0.8680 (p) REVERT: R 242 GLN cc_start: 0.9058 (pp30) cc_final: 0.8786 (pp30) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.1167 time to fit residues: 6.1617 Evaluate side-chains 40 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.080965 restraints weight = 3693.069| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.25 r_work: 0.2821 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2295 Z= 0.160 Angle : 0.536 5.998 3131 Z= 0.259 Chirality : 0.040 0.156 368 Planarity : 0.003 0.029 361 Dihedral : 8.727 59.428 379 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.49 % Allowed : 26.97 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.52), residues: 269 helix: 2.46 (0.35), residues: 217 sheet: None (None), residues: 0 loop : -1.95 (0.77), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.006 0.001 PHE R 64 TYR 0.006 0.001 TYR R 222 ARG 0.002 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.218 Fit side-chains REVERT: R 38 LEU cc_start: 0.8910 (tp) cc_final: 0.8648 (tp) REVERT: R 109 MET cc_start: 0.8886 (ttp) cc_final: 0.8538 (ttm) REVERT: R 166 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8382 (tptt) REVERT: R 201 SER cc_start: 0.9188 (m) cc_final: 0.8684 (p) REVERT: R 242 GLN cc_start: 0.9132 (pp30) cc_final: 0.8849 (pp30) outliers start: 6 outliers final: 5 residues processed: 39 average time/residue: 0.1290 time to fit residues: 6.1544 Evaluate side-chains 39 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.080333 restraints weight = 3666.980| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.27 r_work: 0.2805 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2295 Z= 0.182 Angle : 0.530 6.103 3131 Z= 0.260 Chirality : 0.040 0.157 368 Planarity : 0.003 0.028 361 Dihedral : 8.631 56.657 379 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.49 % Allowed : 26.56 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.53), residues: 269 helix: 2.61 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.95 (0.78), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.006 0.001 PHE R 64 TYR 0.005 0.001 TYR R 279 ARG 0.001 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.231 Fit side-chains REVERT: R 38 LEU cc_start: 0.8911 (tp) cc_final: 0.8619 (tp) REVERT: R 75 ASP cc_start: 0.8902 (m-30) cc_final: 0.8565 (t0) REVERT: R 109 MET cc_start: 0.8922 (ttp) cc_final: 0.8595 (ttm) REVERT: R 143 ARG cc_start: 0.8454 (ptt-90) cc_final: 0.8209 (ptm-80) REVERT: R 166 LYS cc_start: 0.8988 (ttpp) cc_final: 0.8394 (tptt) REVERT: R 201 SER cc_start: 0.9265 (m) cc_final: 0.8735 (p) REVERT: R 242 GLN cc_start: 0.9142 (pp30) cc_final: 0.8835 (pp30) outliers start: 6 outliers final: 6 residues processed: 41 average time/residue: 0.1226 time to fit residues: 6.1648 Evaluate side-chains 41 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.080370 restraints weight = 3745.361| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.28 r_work: 0.2803 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2295 Z= 0.179 Angle : 0.542 6.050 3131 Z= 0.266 Chirality : 0.040 0.157 368 Planarity : 0.003 0.028 361 Dihedral : 8.376 55.508 379 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.90 % Allowed : 27.39 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.53), residues: 269 helix: 2.67 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.90 (0.79), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.006 0.001 PHE R 183 TYR 0.010 0.001 TYR R 279 ARG 0.001 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.227 Fit side-chains REVERT: R 38 LEU cc_start: 0.8920 (tp) cc_final: 0.8627 (tp) REVERT: R 75 ASP cc_start: 0.8911 (m-30) cc_final: 0.8544 (t0) REVERT: R 109 MET cc_start: 0.8917 (ttp) cc_final: 0.8592 (ttm) REVERT: R 166 LYS cc_start: 0.9033 (ttpp) cc_final: 0.8383 (tptt) REVERT: R 201 SER cc_start: 0.9255 (m) cc_final: 0.8733 (p) REVERT: R 242 GLN cc_start: 0.9153 (pp30) cc_final: 0.8850 (pp30) outliers start: 7 outliers final: 6 residues processed: 39 average time/residue: 0.1254 time to fit residues: 6.0077 Evaluate side-chains 39 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.0370 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.081649 restraints weight = 3766.514| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.31 r_work: 0.2826 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2295 Z= 0.152 Angle : 0.522 5.934 3131 Z= 0.256 Chirality : 0.039 0.163 368 Planarity : 0.003 0.028 361 Dihedral : 8.060 55.316 379 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.90 % Allowed : 26.97 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.53), residues: 269 helix: 2.76 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.87 (0.79), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 243 HIS 0.001 0.001 HIS R 144 PHE 0.006 0.001 PHE R 64 TYR 0.010 0.001 TYR R 279 ARG 0.002 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.295 Fit side-chains REVERT: R 38 LEU cc_start: 0.8918 (tp) cc_final: 0.8653 (tp) REVERT: R 75 ASP cc_start: 0.8929 (m-30) cc_final: 0.8582 (t0) REVERT: R 109 MET cc_start: 0.8881 (ttp) cc_final: 0.8525 (ttm) REVERT: R 163 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8336 (tt) REVERT: R 166 LYS cc_start: 0.9000 (ttpp) cc_final: 0.8355 (tptt) REVERT: R 201 SER cc_start: 0.9168 (m) cc_final: 0.8666 (p) REVERT: R 242 GLN cc_start: 0.9144 (pp30) cc_final: 0.8836 (pp30) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.1020 time to fit residues: 5.3003 Evaluate side-chains 39 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 182 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.081122 restraints weight = 3718.158| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.27 r_work: 0.2822 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2295 Z= 0.164 Angle : 0.520 6.017 3131 Z= 0.257 Chirality : 0.040 0.160 368 Planarity : 0.003 0.028 361 Dihedral : 7.959 54.725 379 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.07 % Allowed : 27.39 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.53), residues: 269 helix: 2.78 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.88 (0.79), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.006 0.001 PHE R 64 TYR 0.011 0.001 TYR R 279 ARG 0.002 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.282 Fit side-chains REVERT: R 38 LEU cc_start: 0.8935 (tp) cc_final: 0.8694 (tp) REVERT: R 75 ASP cc_start: 0.8927 (m-30) cc_final: 0.8597 (t0) REVERT: R 109 MET cc_start: 0.8897 (ttp) cc_final: 0.8551 (ttm) REVERT: R 166 LYS cc_start: 0.9028 (ttpp) cc_final: 0.8388 (tptt) REVERT: R 201 SER cc_start: 0.9285 (m) cc_final: 0.8804 (p) REVERT: R 242 GLN cc_start: 0.9164 (pp30) cc_final: 0.8852 (pp30) outliers start: 5 outliers final: 5 residues processed: 38 average time/residue: 0.1210 time to fit residues: 5.7279 Evaluate side-chains 39 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.0270 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.082323 restraints weight = 3681.858| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.26 r_work: 0.2841 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2295 Z= 0.138 Angle : 0.524 5.849 3131 Z= 0.258 Chirality : 0.039 0.167 368 Planarity : 0.003 0.028 361 Dihedral : 7.621 53.860 379 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.49 % Allowed : 27.39 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.53), residues: 269 helix: 2.89 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -1.90 (0.76), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 243 HIS 0.001 0.000 HIS R 261 PHE 0.006 0.001 PHE R 64 TYR 0.010 0.001 TYR R 279 ARG 0.002 0.000 ARG R 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 538 Ramachandran restraints generated. 269 Oldfield, 0 Emsley, 269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.252 Fit side-chains REVERT: R 75 ASP cc_start: 0.8940 (m-30) cc_final: 0.8596 (t0) REVERT: R 109 MET cc_start: 0.8830 (ttp) cc_final: 0.8460 (ttm) REVERT: R 163 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8331 (tt) REVERT: R 166 LYS cc_start: 0.8999 (ttpp) cc_final: 0.8343 (tptt) REVERT: R 201 SER cc_start: 0.9168 (m) cc_final: 0.8685 (p) REVERT: R 242 GLN cc_start: 0.9137 (pp30) cc_final: 0.8824 (pp30) outliers start: 6 outliers final: 5 residues processed: 41 average time/residue: 0.1186 time to fit residues: 6.0613 Evaluate side-chains 42 residues out of total 241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.107450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.081196 restraints weight = 3694.508| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.27 r_work: 0.2824 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2295 Z= 0.168 Angle : 0.539 6.040 3131 Z= 0.264 Chirality : 0.040 0.162 368 Planarity : 0.003 0.028 361 Dihedral : 7.656 53.417 379 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.07 % Allowed : 28.22 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.53), residues: 269 helix: 2.81 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.72 (0.82), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 243 HIS 0.001 0.001 HIS R 261 PHE 0.005 0.001 PHE R 244 TYR 0.011 0.001 TYR R 279 ARG 0.002 0.000 ARG R 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1493.30 seconds wall clock time: 26 minutes 17.99 seconds (1577.99 seconds total)