Starting phenix.real_space_refine on Mon Feb 10 21:59:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypq_34011/02_2025/7ypq_34011.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypq_34011/02_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_34011/02_2025/7ypq_34011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypq_34011/02_2025/7ypq_34011.map" model { file = "/net/cci-nas-00/data/ceres_data/7ypq_34011/02_2025/7ypq_34011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypq_34011/02_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-5592/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: 2.28, per 1000 atoms: 0.78 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: 0.72 Conformation dependent library (CDL) restraints added in 290.0 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: 1.34 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: 0.98 Time building geometry restraints manager: 0.80 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: 0.570 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.820 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- 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 : 0.324 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: 0.1850 time to fit residues: 12.1586 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 : 0.299 ------------------------------------------------------------------------------- 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): 0.3274 rms_B_bonded: 2.13 r_work: 0.3108 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 0.309 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8274 (m110) cc_final: 0.7438 (t0) REVERT: A 130 CYS cc_start: 0.8362 (m) cc_final: 0.8005 (m) REVERT: A 213 LYS cc_start: 0.8438 (mttm) cc_final: 0.7949 (mptt) REVERT: A 262 TYR cc_start: 0.9018 (p90) cc_final: 0.8613 (p90) outliers start: 2 outliers final: 2 residues processed: 48 average time/residue: 0.1658 time to fit residues: 9.5573 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 : 0.293 ------------------------------------------------------------------------------- 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: 0.6980 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.169638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.122847 restraints weight = 2908.650| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.15 r_work: 0.3149 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2990 Z= 0.209 Angle : 0.515 6.318 4081 Z= 0.288 Chirality : 0.042 0.135 459 Planarity : 0.002 0.018 481 Dihedral : 17.736 70.589 510 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.97 % Allowed : 6.77 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.47), residues: 323 helix: 0.98 (0.70), residues: 62 sheet: 0.07 (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 0.007 0.001 PHE A 189 TYR 0.009 0.001 TYR A 299 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 52 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8213 (m110) cc_final: 0.7404 (t0) REVERT: A 130 CYS cc_start: 0.8340 (m) cc_final: 0.8033 (m) REVERT: A 213 LYS cc_start: 0.8415 (mttm) cc_final: 0.7880 (mptt) REVERT: A 262 TYR cc_start: 0.9008 (p90) cc_final: 0.8725 (p90) outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 0.1610 time to fit residues: 9.9566 Evaluate side-chains 46 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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: 0.9980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.166732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.119576 restraints weight = 2962.301| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.18 r_work: 0.3100 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2990 Z= 0.312 Angle : 0.550 5.449 4081 Z= 0.306 Chirality : 0.044 0.144 459 Planarity : 0.003 0.020 481 Dihedral : 17.666 73.421 510 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.75 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: -0.04 (0.47), residues: 323 helix: 1.10 (0.70), residues: 62 sheet: 0.11 (0.46), residues: 120 loop : -0.56 (0.53), residues: 141 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 0.016 0.002 TYR A 260 ARG 0.004 0.001 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 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8175 (m110) cc_final: 0.7341 (t0) REVERT: A 113 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7337 (mp) REVERT: A 130 CYS cc_start: 0.8379 (m) cc_final: 0.8051 (m) REVERT: A 213 LYS cc_start: 0.8476 (mttm) cc_final: 0.7942 (mptt) REVERT: A 262 TYR cc_start: 0.9019 (p90) cc_final: 0.8618 (p90) outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.1718 time to fit residues: 9.7685 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 : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 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 = 0.3783 r_free = 0.3783 target = 0.168057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.121278 restraints weight = 2952.214| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.16 r_work: 0.3106 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1476 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= 0.233 Angle : 0.521 4.966 4081 Z= 0.292 Chirality : 0.042 0.137 459 Planarity : 0.002 0.019 481 Dihedral : 17.630 75.486 510 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.94 % Allowed : 9.35 % Favored : 88.71 % 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: 0.04 (0.47), residues: 323 helix: 1.24 (0.71), residues: 62 sheet: 0.16 (0.46), residues: 120 loop : -0.55 (0.52), 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 0.014 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 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.363 Fit side-chains REVERT: A 80 ASN cc_start: 0.8169 (m110) cc_final: 0.7336 (t0) REVERT: A 99 LYS cc_start: 0.6937 (mmtt) cc_final: 0.6324 (mmmt) REVERT: A 113 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7284 (mp) REVERT: A 130 CYS cc_start: 0.8345 (m) cc_final: 0.8027 (m) REVERT: A 213 LYS cc_start: 0.8484 (mttm) cc_final: 0.7965 (mptt) REVERT: A 262 TYR cc_start: 0.9010 (p90) cc_final: 0.8579 (p90) outliers start: 6 outliers final: 5 residues processed: 47 average time/residue: 0.1725 time to fit residues: 9.8337 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 : 0.343 ------------------------------------------------------------------------------- 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: 4.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.168551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.121611 restraints weight = 2991.645| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.17 r_work: 0.3122 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1594 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= 0.222 Angle : 0.518 6.220 4081 Z= 0.288 Chirality : 0.042 0.139 459 Planarity : 0.002 0.020 481 Dihedral : 17.627 76.374 510 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.26 % Allowed : 9.68 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.47), residues: 323 helix: 1.31 (0.71), residues: 62 sheet: 0.18 (0.47), 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 0.011 0.001 TYR A 260 ARG 0.003 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 : 0.319 Fit side-chains REVERT: A 80 ASN cc_start: 0.8177 (m110) cc_final: 0.7343 (t0) REVERT: A 99 LYS cc_start: 0.6978 (mmtt) cc_final: 0.6380 (mmmt) REVERT: A 113 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7262 (mp) REVERT: A 130 CYS cc_start: 0.8344 (m) cc_final: 0.8030 (m) REVERT: A 213 LYS cc_start: 0.8483 (mttm) cc_final: 0.7978 (mptt) REVERT: A 262 TYR cc_start: 0.9016 (p90) cc_final: 0.8733 (p90) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.1606 time to fit residues: 8.9655 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 : 0.319 ------------------------------------------------------------------------------- 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: 0.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.168917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.121306 restraints weight = 3010.180| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.22 r_work: 0.3155 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1574 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= 0.223 Angle : 0.514 5.920 4081 Z= 0.287 Chirality : 0.042 0.136 459 Planarity : 0.002 0.020 481 Dihedral : 17.620 77.167 510 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.26 % Allowed : 10.65 % Favored : 87.10 % 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: 0.11 (0.47), residues: 323 helix: 1.32 (0.71), residues: 62 sheet: 0.21 (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 0.011 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 52 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.343 Fit side-chains REVERT: A 80 ASN cc_start: 0.8184 (m110) cc_final: 0.7346 (t0) REVERT: A 99 LYS cc_start: 0.6979 (mmtt) cc_final: 0.6362 (mmmt) REVERT: A 113 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7253 (mp) REVERT: A 130 CYS cc_start: 0.8353 (m) cc_final: 0.8033 (m) REVERT: A 213 LYS cc_start: 0.8475 (mttm) cc_final: 0.7958 (mptt) REVERT: A 262 TYR cc_start: 0.9016 (p90) cc_final: 0.8728 (p90) outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 0.1670 time to fit residues: 9.9013 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 : 0.312 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 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: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.169457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.122062 restraints weight = 2907.549| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.20 r_work: 0.3118 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2990 Z= 0.202 Angle : 0.506 5.670 4081 Z= 0.284 Chirality : 0.042 0.135 459 Planarity : 0.002 0.019 481 Dihedral : 17.602 78.410 510 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: 0.19 (0.47), residues: 323 helix: 1.38 (0.71), residues: 62 sheet: 0.42 (0.47), residues: 115 loop : -0.61 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 228 PHE 0.008 0.001 PHE A 258 TYR 0.010 0.001 TYR A 260 ARG 0.003 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 : 0.296 Fit side-chains REVERT: A 80 ASN cc_start: 0.8175 (m110) cc_final: 0.7345 (t0) REVERT: A 99 LYS cc_start: 0.6916 (mmtt) cc_final: 0.6319 (mmmt) REVERT: A 113 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7173 (mp) REVERT: A 130 CYS cc_start: 0.8324 (m) cc_final: 0.8004 (m) REVERT: A 213 LYS cc_start: 0.8455 (mttm) cc_final: 0.7960 (mptt) REVERT: A 262 TYR cc_start: 0.9000 (p90) cc_final: 0.8701 (p90) outliers start: 7 outliers final: 5 residues processed: 46 average time/residue: 0.1663 time to fit residues: 9.3573 Evaluate side-chains 46 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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: 0.0000 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.169473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.122224 restraints weight = 2907.120| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.19 r_work: 0.3120 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2990 Z= 0.209 Angle : 0.514 5.477 4081 Z= 0.289 Chirality : 0.042 0.136 459 Planarity : 0.002 0.019 481 Dihedral : 17.606 78.929 510 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.94 % Allowed : 12.26 % 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: 0.18 (0.47), residues: 323 helix: 1.40 (0.71), residues: 62 sheet: 0.35 (0.46), residues: 118 loop : -0.58 (0.52), residues: 143 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 0.010 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 47 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.344 Fit side-chains REVERT: A 80 ASN cc_start: 0.8156 (m110) cc_final: 0.7328 (t0) REVERT: A 99 LYS cc_start: 0.6932 (mmtt) cc_final: 0.6352 (mmmt) REVERT: A 113 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7209 (mp) REVERT: A 130 CYS cc_start: 0.8318 (m) cc_final: 0.7999 (m) REVERT: A 213 LYS cc_start: 0.8478 (mttm) cc_final: 0.8011 (mptt) REVERT: A 262 TYR cc_start: 0.9001 (p90) cc_final: 0.8694 (p90) outliers start: 6 outliers final: 5 residues processed: 44 average time/residue: 0.1723 time to fit residues: 9.2898 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 : 0.315 ------------------------------------------------------------------------------- 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: 3.9990 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 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 = 0.168490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.121727 restraints weight = 2955.251| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.18 r_work: 0.3120 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2990 Z= 0.240 Angle : 0.518 5.458 4081 Z= 0.289 Chirality : 0.042 0.140 459 Planarity : 0.002 0.019 481 Dihedral : 17.617 79.484 510 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: 0.17 (0.47), residues: 323 helix: 1.38 (0.71), residues: 62 sheet: 0.34 (0.47), residues: 118 loop : -0.58 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 228 PHE 0.009 0.001 PHE A 258 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 : 0.321 Fit side-chains REVERT: A 80 ASN cc_start: 0.8164 (m110) cc_final: 0.7330 (t0) REVERT: A 99 LYS cc_start: 0.6935 (mmtt) cc_final: 0.6339 (mmmt) REVERT: A 113 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7218 (mp) REVERT: A 130 CYS cc_start: 0.8353 (m) cc_final: 0.8023 (m) REVERT: A 213 LYS cc_start: 0.8476 (mttm) cc_final: 0.8013 (mptt) REVERT: A 262 TYR cc_start: 0.8999 (p90) cc_final: 0.8690 (p90) outliers start: 6 outliers final: 5 residues processed: 44 average time/residue: 0.1651 time to fit residues: 8.9207 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 : 0.339 ------------------------------------------------------------------------------- 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: 8.9990 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.167080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.119962 restraints weight = 2938.951| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.17 r_work: 0.3102 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2990 Z= 0.301 Angle : 0.545 5.502 4081 Z= 0.304 Chirality : 0.043 0.141 459 Planarity : 0.002 0.019 481 Dihedral : 17.657 81.005 510 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.26 % Allowed : 12.58 % 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: 0.12 (0.47), residues: 323 helix: 1.33 (0.71), residues: 62 sheet: 0.32 (0.47), residues: 118 loop : -0.62 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 276 PHE 0.010 0.001 PHE A 189 TYR 0.010 0.001 TYR A 351 ARG 0.004 0.000 ARG A 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1643.01 seconds wall clock time: 29 minutes 56.89 seconds (1796.89 seconds total)