Starting phenix.real_space_refine on Wed Mar 5 16:58:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypq_34011/03_2025/7ypq_34011.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypq_34011/03_2025/7ypq_34011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ypq_34011/03_2025/7ypq_34011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypq_34011/03_2025/7ypq_34011.map" model { file = "/net/cci-nas-00/data/ceres_data/7ypq_34011/03_2025/7ypq_34011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypq_34011/03_2025/7ypq_34011.cif" } resolution = 3.1 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= 0.002 sd= 0.137 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 P 11 5.49 5 S 12 5.16 5 C 1811 2.51 5 N 493 2.21 5 O 588 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: 2915 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2684 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 324} Chain breaks: 1 Chain: "Q" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Time building chain proxies: 2.52, per 1000 atoms: 0.86 Number of scatterers: 2915 At special positions: 0 Unit cell: (65.55, 79.8, 75.05, 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) S 12 16.00 P 11 15.00 O 588 8.00 N 493 7.00 C 1811 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: 0.73 Conformation dependent library (CDL) restraints added in 337.5 milliseconds 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 634 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 4 sheets defined 18.7% alpha, 48.6% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.742A pdb=" N PHE A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 Processing helix chain 'A' and resid 319 through 336 Processing helix chain 'A' and resid 336 through 343 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 66 removed outlier: 6.671A pdb=" N LYS A 75 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS A 61 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 73 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR A 63 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR A 71 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER A 65 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 72 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 12.776A pdb=" N LEU A 112 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASP A 84 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE A 114 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR A 86 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N SER A 116 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER A 108 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE A 114 " --> pdb=" O GLN A 106 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLN A 106 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 116 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 8.221A pdb=" N LEU A 236 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLU A 184 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU A 238 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET A 186 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N SER A 240 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 10.998A pdb=" N SER A 239 " --> pdb=" O CYS A 226 " (cutoff:3.500A) removed outlier: 11.082A pdb=" N CYS A 226 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N ASN A 241 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 224 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 217 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS A 144 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 14.863A pdb=" N LEU A 146 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 13.885A pdb=" N GLU A 172 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ALA A 148 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU A 170 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N PHE A 150 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 168 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 152 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 278 removed outlier: 4.579A pdb=" N VAL A 348 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN A 347 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS A 369 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP A 349 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE A 367 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR A 351 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 288 102 hydrogen bonds defined for protein. 291 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 0.87 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: 919 1.34 - 1.46: 637 1.46 - 1.57: 1394 1.57 - 1.69: 21 1.69 - 1.81: 19 Bond restraints: 2990 Sorted by residual: bond pdb=" C LEU A 165 " pdb=" N VAL A 166 " ideal model delta sigma weight residual 1.330 1.302 0.028 1.26e-02 6.30e+03 4.94e+00 bond pdb=" CG LEU A 379 " pdb=" CD1 LEU A 379 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" CB VAL A 183 " pdb=" CG2 VAL A 183 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.50e-01 bond pdb=" CG LEU A 352 " pdb=" CD1 LEU A 352 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.74e-01 bond pdb=" CB VAL A 166 " pdb=" CG1 VAL A 166 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.50e-01 ... (remaining 2985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 3893 1.32 - 2.65: 154 2.65 - 3.97: 27 3.97 - 5.29: 5 5.29 - 6.62: 2 Bond angle restraints: 4081 Sorted by residual: angle pdb=" CA GLU A 216 " pdb=" CB GLU A 216 " pdb=" CG GLU A 216 " ideal model delta sigma weight residual 114.10 119.08 -4.98 2.00e+00 2.50e-01 6.21e+00 angle pdb=" C MET A 253 " pdb=" CA MET A 253 " pdb=" CB MET A 253 " ideal model delta sigma weight residual 111.41 115.04 -3.63 1.70e+00 3.46e-01 4.55e+00 angle pdb=" C ASP A 293 " pdb=" N ARG A 294 " pdb=" CA ARG A 294 " ideal model delta sigma weight residual 122.62 119.34 3.28 1.56e+00 4.11e-01 4.43e+00 angle pdb=" CG1 VAL A 359 " pdb=" CB VAL A 359 " pdb=" CG2 VAL A 359 " ideal model delta sigma weight residual 110.80 106.25 4.55 2.20e+00 2.07e-01 4.28e+00 angle pdb=" N ASN A 161 " pdb=" CA ASN A 161 " pdb=" C ASN A 161 " ideal model delta sigma weight residual 110.80 115.15 -4.35 2.13e+00 2.20e-01 4.16e+00 ... (remaining 4076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1553 17.98 - 35.96: 180 35.96 - 53.94: 56 53.94 - 71.92: 12 71.92 - 89.90: 4 Dihedral angle restraints: 1805 sinusoidal: 823 harmonic: 982 Sorted by residual: dihedral pdb=" CA TYR A 351 " pdb=" C TYR A 351 " pdb=" N LEU A 352 " pdb=" CA LEU A 352 " ideal model delta harmonic sigma weight residual -180.00 -156.65 -23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE A 219 " pdb=" C PHE A 219 " pdb=" N ASN A 220 " pdb=" CA ASN A 220 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLU A 304 " pdb=" C GLU A 304 " pdb=" N LYS A 305 " pdb=" CA LYS A 305 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 1802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 260 0.031 - 0.062: 131 0.062 - 0.092: 35 0.092 - 0.123: 28 0.123 - 0.154: 5 Chirality restraints: 459 Sorted by residual: chirality pdb=" CA ILE A 310 " pdb=" N ILE A 310 " pdb=" C ILE A 310 " pdb=" CB ILE A 310 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA VAL A 183 " pdb=" N VAL A 183 " pdb=" C VAL A 183 " pdb=" CB VAL A 183 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE A 370 " pdb=" N ILE A 370 " pdb=" C ILE A 370 " pdb=" CB ILE A 370 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 456 not shown) Planarity restraints: 481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 377 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO A 378 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 216 " 0.004 2.00e-02 2.50e+03 7.45e-03 5.55e-01 pdb=" C GLU A 216 " -0.013 2.00e-02 2.50e+03 pdb=" O GLU A 216 " 0.005 2.00e-02 2.50e+03 pdb=" N LYS A 217 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 297 " 0.004 2.00e-02 2.50e+03 7.39e-03 5.46e-01 pdb=" C ILE A 297 " -0.013 2.00e-02 2.50e+03 pdb=" O ILE A 297 " 0.005 2.00e-02 2.50e+03 pdb=" N SER A 298 " 0.004 2.00e-02 2.50e+03 ... (remaining 478 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 611 2.79 - 3.32: 2563 3.32 - 3.84: 4682 3.84 - 4.37: 5819 4.37 - 4.90: 9706 Nonbonded interactions: 23381 Sorted by model distance: nonbonded pdb=" O CYS A 210 " pdb=" OG SER A 214 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASN A 98 " pdb=" NE2 GLN A 243 " model vdw 2.360 3.120 nonbonded pdb=" OG SER A 292 " pdb=" OP1 DA Q 9 " model vdw 2.402 3.040 nonbonded pdb=" NH2 ARG A 223 " pdb=" O ASN A 241 " model vdw 2.413 3.120 nonbonded pdb=" O ASN A 358 " pdb=" OD1 ASN A 358 " model vdw 2.421 3.040 ... (remaining 23376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.200 Find NCS groups from input model: 0.030 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 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 : 0.005 0.041 2990 Z= 0.314 Angle : 0.632 6.618 4081 Z= 0.360 Chirality : 0.046 0.154 459 Planarity : 0.002 0.029 481 Dihedral : 17.794 89.903 1171 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -0.66 (0.46), residues: 323 helix: 0.04 (0.66), residues: 62 sheet: -0.22 (0.45), residues: 125 loop : -0.73 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 228 PHE 0.008 0.001 PHE A 189 TYR 0.010 0.001 TYR A 299 ARG 0.004 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.327 Fit side-chains REVERT: A 80 ASN cc_start: 0.8098 (m110) cc_final: 0.7333 (t0) REVERT: A 130 CYS cc_start: 0.8140 (m) cc_final: 0.7935 (m) REVERT: A 206 ASP cc_start: 0.7749 (m-30) cc_final: 0.7522 (m-30) REVERT: A 262 TYR cc_start: 0.8966 (p90) cc_final: 0.8652 (p90) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1730 time to fit residues: 11.4137 Evaluate side-chains 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.168147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.121715 restraints weight = 2955.397| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.13 r_work: 0.3109 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2990 Z= 0.257 Angle : 0.583 8.302 4081 Z= 0.321 Chirality : 0.045 0.136 459 Planarity : 0.003 0.022 481 Dihedral : 17.027 70.211 510 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.65 % Allowed : 4.52 % Favored : 94.84 % 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: -0.30 (0.47), residues: 323 helix: 0.68 (0.70), residues: 62 sheet: -0.04 (0.46), residues: 123 loop : -0.63 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 276 PHE 0.009 0.001 PHE A 189 TYR 0.009 0.001 TYR A 351 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8274 (m110) cc_final: 0.7439 (t0) REVERT: A 130 CYS cc_start: 0.8363 (m) cc_final: 0.8008 (m) REVERT: A 213 LYS cc_start: 0.8436 (mttm) cc_final: 0.7953 (mptt) REVERT: A 262 TYR cc_start: 0.9019 (p90) cc_final: 0.8615 (p90) outliers start: 2 outliers final: 2 residues processed: 48 average time/residue: 0.1693 time to fit residues: 9.7887 Evaluate side-chains 45 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 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 = 0.3791 r_free = 0.3791 target = 0.169031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.122067 restraints weight = 2909.227| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.16 r_work: 0.3128 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2990 Z= 0.231 Angle : 0.524 6.220 4081 Z= 0.293 Chirality : 0.043 0.136 459 Planarity : 0.002 0.019 481 Dihedral : 17.763 70.847 510 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.97 % Allowed : 7.10 % Favored : 91.94 % 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: -0.10 (0.47), residues: 323 helix: 0.95 (0.69), residues: 62 sheet: 0.05 (0.46), residues: 120 loop : -0.53 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 228 PHE 0.008 0.001 PHE A 189 TYR 0.009 0.001 TYR A 260 ARG 0.003 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8214 (m110) cc_final: 0.7391 (t0) REVERT: A 130 CYS cc_start: 0.8356 (m) cc_final: 0.8040 (m) REVERT: A 213 LYS cc_start: 0.8424 (mttm) cc_final: 0.7881 (mptt) REVERT: A 262 TYR cc_start: 0.9009 (p90) cc_final: 0.8588 (p90) outliers start: 3 outliers final: 3 residues processed: 52 average time/residue: 0.1673 time to fit residues: 10.5226 Evaluate side-chains 47 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 31 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 = 0.3781 r_free = 0.3781 target = 0.167769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120742 restraints weight = 2950.630| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.17 r_work: 0.3107 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2990 Z= 0.266 Angle : 0.533 5.759 4081 Z= 0.295 Chirality : 0.043 0.140 459 Planarity : 0.002 0.019 481 Dihedral : 17.678 72.576 510 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.61 % Allowed : 9.03 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.47), residues: 323 helix: 1.18 (0.70), residues: 62 sheet: 0.13 (0.46), residues: 120 loop : -0.54 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 276 PHE 0.008 0.001 PHE A 189 TYR 0.016 0.001 TYR A 260 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8158 (m110) cc_final: 0.7340 (t0) REVERT: A 113 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7310 (mp) REVERT: A 130 CYS cc_start: 0.8358 (m) cc_final: 0.8046 (m) REVERT: A 213 LYS cc_start: 0.8482 (mttm) cc_final: 0.7955 (mptt) REVERT: A 262 TYR cc_start: 0.9017 (p90) cc_final: 0.8595 (p90) outliers start: 5 outliers final: 4 residues processed: 46 average time/residue: 0.1784 time to fit residues: 9.9023 Evaluate side-chains 46 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 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 = 0.3790 r_free = 0.3790 target = 0.168646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.121336 restraints weight = 2952.407| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.19 r_work: 0.3141 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2990 Z= 0.234 Angle : 0.520 5.339 4081 Z= 0.290 Chirality : 0.043 0.139 459 Planarity : 0.002 0.019 481 Dihedral : 17.642 73.834 510 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.94 % Allowed : 9.03 % Favored : 89.03 % 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: 0.06 (0.47), residues: 323 helix: 1.26 (0.71), residues: 62 sheet: 0.17 (0.46), residues: 120 loop : -0.53 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 228 PHE 0.008 0.001 PHE A 189 TYR 0.014 0.001 TYR A 260 ARG 0.003 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8165 (m110) cc_final: 0.7342 (t0) REVERT: A 113 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7273 (mp) REVERT: A 130 CYS cc_start: 0.8352 (m) cc_final: 0.8043 (m) REVERT: A 213 LYS cc_start: 0.8473 (mttm) cc_final: 0.7958 (mptt) REVERT: A 262 TYR cc_start: 0.9020 (p90) cc_final: 0.8593 (p90) outliers start: 6 outliers final: 5 residues processed: 46 average time/residue: 0.1798 time to fit residues: 9.8991 Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.168764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.121173 restraints weight = 2992.366| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.21 r_work: 0.3113 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2990 Z= 0.238 Angle : 0.516 4.832 4081 Z= 0.289 Chirality : 0.043 0.148 459 Planarity : 0.002 0.019 481 Dihedral : 17.640 74.646 510 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.26 % Allowed : 9.35 % Favored : 88.39 % 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: 0.10 (0.47), residues: 323 helix: 1.29 (0.71), residues: 62 sheet: 0.21 (0.47), residues: 120 loop : -0.52 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 228 PHE 0.008 0.001 PHE A 189 TYR 0.012 0.001 TYR A 260 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8174 (m110) cc_final: 0.7339 (t0) REVERT: A 113 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7272 (mp) REVERT: A 130 CYS cc_start: 0.8343 (m) cc_final: 0.8026 (m) REVERT: A 213 LYS cc_start: 0.8470 (mttm) cc_final: 0.7968 (mptt) REVERT: A 262 TYR cc_start: 0.9019 (p90) cc_final: 0.8741 (p90) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.1678 time to fit residues: 9.3197 Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.168323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121446 restraints weight = 3013.082| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.18 r_work: 0.3126 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2990 Z= 0.226 Angle : 0.510 4.332 4081 Z= 0.286 Chirality : 0.042 0.137 459 Planarity : 0.002 0.018 481 Dihedral : 17.631 75.423 510 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.58 % Allowed : 10.00 % Favored : 87.42 % 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: 0.12 (0.47), residues: 323 helix: 1.33 (0.71), residues: 62 sheet: 0.22 (0.46), residues: 120 loop : -0.52 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 228 PHE 0.008 0.001 PHE A 189 TYR 0.011 0.001 TYR A 260 ARG 0.003 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.337 Fit side-chains REVERT: A 80 ASN cc_start: 0.8173 (m110) cc_final: 0.7345 (t0) REVERT: A 99 LYS cc_start: 0.6964 (mmtt) cc_final: 0.6359 (mmmt) REVERT: A 113 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7251 (mp) REVERT: A 130 CYS cc_start: 0.8339 (m) cc_final: 0.8026 (m) REVERT: A 213 LYS cc_start: 0.8468 (mttm) cc_final: 0.7975 (mptt) REVERT: A 262 TYR cc_start: 0.9018 (p90) cc_final: 0.8736 (p90) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.1714 time to fit residues: 9.9733 Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.168742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121445 restraints weight = 2913.229| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.19 r_work: 0.3120 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2990 Z= 0.235 Angle : 0.514 5.176 4081 Z= 0.289 Chirality : 0.042 0.152 459 Planarity : 0.002 0.019 481 Dihedral : 17.633 76.313 510 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.26 % Allowed : 11.61 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.47), residues: 323 helix: 1.34 (0.71), residues: 62 sheet: 0.24 (0.47), residues: 120 loop : -0.52 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 228 PHE 0.008 0.001 PHE A 189 TYR 0.010 0.001 TYR A 260 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.304 Fit side-chains REVERT: A 80 ASN cc_start: 0.8183 (m110) cc_final: 0.7343 (t0) REVERT: A 99 LYS cc_start: 0.6986 (mmtt) cc_final: 0.6369 (mmmt) REVERT: A 113 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7174 (mp) REVERT: A 130 CYS cc_start: 0.8340 (m) cc_final: 0.8015 (m) REVERT: A 213 LYS cc_start: 0.8483 (mttm) cc_final: 0.7999 (mptt) REVERT: A 262 TYR cc_start: 0.9018 (p90) cc_final: 0.8732 (p90) outliers start: 7 outliers final: 5 residues processed: 46 average time/residue: 0.1677 time to fit residues: 9.3361 Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 10 optimal weight: 0.0870 chunk 28 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.170258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.123910 restraints weight = 2905.374| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.17 r_work: 0.3158 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2990 Z= 0.173 Angle : 0.490 4.378 4081 Z= 0.279 Chirality : 0.041 0.133 459 Planarity : 0.002 0.018 481 Dihedral : 17.587 78.072 510 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.26 % Allowed : 11.94 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.25 (0.47), residues: 323 helix: 1.43 (0.71), residues: 62 sheet: 0.47 (0.47), residues: 115 loop : -0.58 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 228 PHE 0.006 0.001 PHE A 189 TYR 0.009 0.001 TYR A 260 ARG 0.003 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.313 Fit side-chains REVERT: A 80 ASN cc_start: 0.8134 (m110) cc_final: 0.7316 (t0) REVERT: A 99 LYS cc_start: 0.6975 (mmtt) cc_final: 0.6376 (mmmt) REVERT: A 113 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7168 (mp) REVERT: A 130 CYS cc_start: 0.8305 (m) cc_final: 0.7989 (m) REVERT: A 213 LYS cc_start: 0.8444 (mttm) cc_final: 0.7973 (mptt) REVERT: A 262 TYR cc_start: 0.8977 (p90) cc_final: 0.8679 (p90) outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 0.1700 time to fit residues: 10.4506 Evaluate side-chains 47 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.169895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.123153 restraints weight = 2951.686| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.19 r_work: 0.3145 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2990 Z= 0.206 Angle : 0.498 4.777 4081 Z= 0.281 Chirality : 0.042 0.135 459 Planarity : 0.002 0.018 481 Dihedral : 17.615 78.767 510 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.94 % Allowed : 12.58 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.47), residues: 323 helix: 1.45 (0.71), residues: 62 sheet: 0.35 (0.46), residues: 120 loop : -0.53 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 228 PHE 0.007 0.001 PHE A 189 TYR 0.009 0.001 TYR A 260 ARG 0.003 0.000 ARG A 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.299 Fit side-chains REVERT: A 80 ASN cc_start: 0.8143 (m110) cc_final: 0.7344 (t0) REVERT: A 99 LYS cc_start: 0.6970 (mmtt) cc_final: 0.6393 (mmmt) REVERT: A 113 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7204 (mp) REVERT: A 130 CYS cc_start: 0.8315 (m) cc_final: 0.8004 (m) REVERT: A 213 LYS cc_start: 0.8478 (mttm) cc_final: 0.8031 (mptt) REVERT: A 262 TYR cc_start: 0.8998 (p90) cc_final: 0.8701 (p90) outliers start: 6 outliers final: 5 residues processed: 44 average time/residue: 0.1654 time to fit residues: 8.8933 Evaluate side-chains 47 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.0020 chunk 15 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.169437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.122934 restraints weight = 2925.522| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.18 r_work: 0.3137 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2990 Z= 0.208 Angle : 0.498 4.454 4081 Z= 0.282 Chirality : 0.042 0.136 459 Planarity : 0.002 0.018 481 Dihedral : 17.609 79.197 510 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.94 % Allowed : 12.90 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.47), residues: 323 helix: 1.50 (0.71), residues: 62 sheet: 0.35 (0.46), residues: 120 loop : -0.54 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 228 PHE 0.007 0.001 PHE A 189 TYR 0.009 0.001 TYR A 260 ARG 0.003 0.000 ARG A 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1793.19 seconds wall clock time: 31 minutes 32.55 seconds (1892.55 seconds total)