Starting phenix.real_space_refine on Mon Feb 10 21:40:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x3k_38038/02_2025/8x3k_38038.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x3k_38038/02_2025/8x3k_38038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x3k_38038/02_2025/8x3k_38038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x3k_38038/02_2025/8x3k_38038.map" model { file = "/net/cci-nas-00/data/ceres_data/8x3k_38038/02_2025/8x3k_38038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x3k_38038/02_2025/8x3k_38038.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.120 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 1865 2.51 5 N 434 2.21 5 O 470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 2797 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2784 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 23, 'TRANS': 349} Chain breaks: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.60, per 1000 atoms: 0.93 Number of scatterers: 2797 At special positions: 0 Unit cell: (68.968, 54.056, 62.444, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 470 8.00 N 434 7.00 C 1865 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: 0.83 Conformation dependent library (CDL) restraints added in 372.1 milliseconds 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 670 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 90.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 18 through 41 removed outlier: 3.918A pdb=" N ILE A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 157 removed outlier: 4.442A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 4.131A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.889A pdb=" N GLY A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS A 167 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 Processing helix chain 'A' and resid 213 through 234 removed outlier: 3.781A pdb=" N ASN A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 removed outlier: 3.708A pdb=" N PHE A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 270 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 323 Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix removed outlier: 4.069A pdb=" N GLU A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.799A pdb=" N SER A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 374 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 385 through 413 removed outlier: 3.990A pdb=" N SER A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 418 through 448 removed outlier: 3.972A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 233 hydrogen bonds defined for protein. 681 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 544 1.33 - 1.45: 629 1.45 - 1.57: 1644 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 2865 Sorted by residual: bond pdb=" CA SER A 197 " pdb=" C SER A 197 " ideal model delta sigma weight residual 1.524 1.488 0.035 1.27e-02 6.20e+03 7.79e+00 bond pdb=" CA SRO A 601 " pdb=" NZ SRO A 601 " ideal model delta sigma weight residual 1.469 1.520 -0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" C ILE A 301 " pdb=" O ILE A 301 " ideal model delta sigma weight residual 1.237 1.208 0.029 1.17e-02 7.31e+03 6.15e+00 bond pdb=" CA SER A 209 " pdb=" C SER A 209 " ideal model delta sigma weight residual 1.523 1.489 0.033 1.37e-02 5.33e+03 5.95e+00 bond pdb=" CA LYS A 281 " pdb=" C LYS A 281 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.35e-02 5.49e+03 5.21e+00 ... (remaining 2860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 3716 1.80 - 3.59: 139 3.59 - 5.39: 27 5.39 - 7.18: 10 7.18 - 8.98: 4 Bond angle restraints: 3896 Sorted by residual: angle pdb=" N VAL A 427 " pdb=" CA VAL A 427 " pdb=" C VAL A 427 " ideal model delta sigma weight residual 111.00 106.06 4.94 1.09e+00 8.42e-01 2.05e+01 angle pdb=" N ARG A 274 " pdb=" CA ARG A 274 " pdb=" C ARG A 274 " ideal model delta sigma weight residual 109.95 116.99 -7.04 1.59e+00 3.96e-01 1.96e+01 angle pdb=" N VAL A 417 " pdb=" CA VAL A 417 " pdb=" C VAL A 417 " ideal model delta sigma weight residual 108.12 102.08 6.04 1.44e+00 4.82e-01 1.76e+01 angle pdb=" N ILE A 405 " pdb=" CA ILE A 405 " pdb=" C ILE A 405 " ideal model delta sigma weight residual 111.44 106.40 5.04 1.34e+00 5.57e-01 1.41e+01 angle pdb=" N SER A 199 " pdb=" CA SER A 199 " pdb=" C SER A 199 " ideal model delta sigma weight residual 111.82 116.09 -4.27 1.16e+00 7.43e-01 1.36e+01 ... (remaining 3891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.76: 1437 12.76 - 25.52: 160 25.52 - 38.28: 56 38.28 - 51.04: 17 51.04 - 63.81: 7 Dihedral angle restraints: 1677 sinusoidal: 625 harmonic: 1052 Sorted by residual: dihedral pdb=" CA TYR A 422 " pdb=" C TYR A 422 " pdb=" N ALA A 423 " pdb=" CA ALA A 423 " ideal model delta harmonic sigma weight residual 180.00 163.36 16.64 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ASN A 146 " pdb=" CB ASN A 146 " pdb=" CG ASN A 146 " pdb=" OD1 ASN A 146 " ideal model delta sinusoidal sigma weight residual 120.00 -176.19 -63.81 2 2.00e+01 2.50e-03 9.66e+00 dihedral pdb=" CA ASP A 213 " pdb=" CB ASP A 213 " pdb=" CG ASP A 213 " pdb=" OD1 ASP A 213 " ideal model delta sinusoidal sigma weight residual -30.00 -82.99 52.99 1 2.00e+01 2.50e-03 9.55e+00 ... (remaining 1674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 250 0.030 - 0.059: 131 0.059 - 0.089: 52 0.089 - 0.119: 24 0.119 - 0.149: 8 Chirality restraints: 465 Sorted by residual: chirality pdb=" CA PRO A 159 " pdb=" N PRO A 159 " pdb=" C PRO A 159 " pdb=" CB PRO A 159 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA PHE A 348 " pdb=" N PHE A 348 " pdb=" C PHE A 348 " pdb=" CB PHE A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA SER A 199 " pdb=" N SER A 199 " pdb=" C SER A 199 " pdb=" CB SER A 199 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 462 not shown) Planarity restraints: 476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 164 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C ALA A 164 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA A 164 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 165 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 236 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 404 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C PRO A 404 " -0.025 2.00e-02 2.50e+03 pdb=" O PRO A 404 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 405 " 0.009 2.00e-02 2.50e+03 ... (remaining 473 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 641 2.77 - 3.30: 2781 3.30 - 3.84: 4751 3.84 - 4.37: 5519 4.37 - 4.90: 9726 Nonbonded interactions: 23418 Sorted by model distance: nonbonded pdb=" O ILE A 301 " pdb=" ND2 ASN A 305 " model vdw 2.238 3.120 nonbonded pdb=" O THR A 212 " pdb=" OG1 THR A 212 " model vdw 2.326 3.040 nonbonded pdb=" O PRO A 336 " pdb=" OG SER A 340 " model vdw 2.418 3.040 nonbonded pdb=" NH2 ARG A 19 " pdb=" OE1 GLU A 216 " model vdw 2.465 3.120 nonbonded pdb=" OE1 GLU A 215 " pdb=" ND1 HIS A 353 " model vdw 2.481 3.120 ... (remaining 23413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.090 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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 : 0.008 0.058 2865 Z= 0.485 Angle : 0.905 8.976 3896 Z= 0.521 Chirality : 0.046 0.149 465 Planarity : 0.005 0.037 476 Dihedral : 13.537 63.806 1007 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.34 % Allowed : 14.77 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.39), residues: 369 helix: -1.07 (0.27), residues: 297 sheet: None (None), residues: 0 loop : -2.46 (0.62), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.003 0.001 HIS A 353 PHE 0.015 0.002 PHE A 348 TYR 0.018 0.002 TYR A 422 ARG 0.002 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.330 Fit side-chains REVERT: A 151 LEU cc_start: 0.8060 (mt) cc_final: 0.7827 (mp) REVERT: A 166 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.6340 (t80) REVERT: A 310 MET cc_start: 0.8148 (mtt) cc_final: 0.7878 (mtp) REVERT: A 453 MET cc_start: 0.7412 (mmp) cc_final: 0.6925 (mmp) outliers start: 4 outliers final: 1 residues processed: 54 average time/residue: 0.8025 time to fit residues: 45.0410 Evaluate side-chains 46 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 146 ASN A 346 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.149370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.130319 restraints weight = 3193.758| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.09 r_work: 0.3493 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2865 Z= 0.264 Angle : 0.653 7.397 3896 Z= 0.331 Chirality : 0.042 0.126 465 Planarity : 0.005 0.037 476 Dihedral : 6.694 61.456 397 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.03 % Allowed : 17.11 % Favored : 78.86 % 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: -0.13 (0.43), residues: 369 helix: 0.40 (0.29), residues: 306 sheet: None (None), residues: 0 loop : -2.12 (0.65), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.012 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.300 Fit side-chains REVERT: A 151 LEU cc_start: 0.8154 (mt) cc_final: 0.7911 (mp) REVERT: A 181 SER cc_start: 0.7379 (OUTLIER) cc_final: 0.6666 (p) REVERT: A 310 MET cc_start: 0.8300 (mtt) cc_final: 0.8099 (mtp) REVERT: A 453 MET cc_start: 0.7735 (mmp) cc_final: 0.7248 (mmp) outliers start: 12 outliers final: 6 residues processed: 49 average time/residue: 0.8757 time to fit residues: 44.5452 Evaluate side-chains 51 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 431 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 30 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.153505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.134780 restraints weight = 3085.051| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.01 r_work: 0.3564 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2865 Z= 0.203 Angle : 0.598 6.715 3896 Z= 0.300 Chirality : 0.040 0.122 465 Planarity : 0.005 0.036 476 Dihedral : 6.342 65.746 395 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.68 % Allowed : 19.46 % Favored : 77.85 % 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: 0.89 (0.44), residues: 369 helix: 1.03 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -1.53 (0.69), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.012 0.001 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.305 Fit side-chains REVERT: A 151 LEU cc_start: 0.8136 (mt) cc_final: 0.7893 (mp) REVERT: A 233 LEU cc_start: 0.7939 (tt) cc_final: 0.7709 (tp) REVERT: A 453 MET cc_start: 0.7666 (mmp) cc_final: 0.7269 (mmp) outliers start: 8 outliers final: 3 residues processed: 50 average time/residue: 0.8682 time to fit residues: 45.0701 Evaluate side-chains 49 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 0.1980 chunk 2 optimal weight: 0.0060 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.153424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134384 restraints weight = 3246.356| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.10 r_work: 0.3568 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2865 Z= 0.204 Angle : 0.594 6.672 3896 Z= 0.295 Chirality : 0.041 0.123 465 Planarity : 0.005 0.037 476 Dihedral : 6.273 66.175 395 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.69 % Allowed : 20.81 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.44), residues: 369 helix: 1.28 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -1.25 (0.69), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.011 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.268 Fit side-chains REVERT: A 151 LEU cc_start: 0.8033 (mt) cc_final: 0.7780 (mp) REVERT: A 233 LEU cc_start: 0.7779 (tt) cc_final: 0.7516 (mt) REVERT: A 453 MET cc_start: 0.7625 (mmp) cc_final: 0.7223 (mmp) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.8852 time to fit residues: 45.9574 Evaluate side-chains 52 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 21 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.158768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.138557 restraints weight = 3196.051| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.18 r_work: 0.3569 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2865 Z= 0.227 Angle : 0.599 6.823 3896 Z= 0.298 Chirality : 0.042 0.159 465 Planarity : 0.005 0.034 476 Dihedral : 6.337 67.974 395 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.70 % Allowed : 20.47 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.44), residues: 369 helix: 1.42 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -0.98 (0.73), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.002 0.001 HIS A 353 PHE 0.011 0.001 PHE A 348 TYR 0.015 0.001 TYR A 422 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.380 Fit side-chains REVERT: A 151 LEU cc_start: 0.8056 (mt) cc_final: 0.7804 (mp) REVERT: A 181 SER cc_start: 0.7370 (OUTLIER) cc_final: 0.6573 (p) REVERT: A 233 LEU cc_start: 0.7732 (tt) cc_final: 0.7471 (mt) REVERT: A 453 MET cc_start: 0.7511 (mmp) cc_final: 0.6992 (mmp) outliers start: 14 outliers final: 7 residues processed: 51 average time/residue: 0.8365 time to fit residues: 44.5176 Evaluate side-chains 54 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 13 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.159435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139322 restraints weight = 3240.911| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.19 r_work: 0.3581 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2865 Z= 0.219 Angle : 0.602 6.838 3896 Z= 0.300 Chirality : 0.042 0.140 465 Planarity : 0.005 0.034 476 Dihedral : 6.315 68.526 395 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.69 % Allowed : 21.14 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.44), residues: 369 helix: 1.48 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -0.90 (0.74), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.002 0.001 HIS A 353 PHE 0.012 0.001 PHE A 348 TYR 0.015 0.001 TYR A 422 ARG 0.000 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.291 Fit side-chains REVERT: A 151 LEU cc_start: 0.8092 (mt) cc_final: 0.7829 (mp) REVERT: A 181 SER cc_start: 0.7451 (OUTLIER) cc_final: 0.6654 (p) REVERT: A 233 LEU cc_start: 0.7691 (tt) cc_final: 0.7447 (mt) REVERT: A 453 MET cc_start: 0.7550 (mmp) cc_final: 0.7012 (mmp) outliers start: 11 outliers final: 8 residues processed: 51 average time/residue: 0.8036 time to fit residues: 42.6244 Evaluate side-chains 54 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.156963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136648 restraints weight = 3288.478| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.18 r_work: 0.3529 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2865 Z= 0.276 Angle : 0.628 6.913 3896 Z= 0.313 Chirality : 0.043 0.131 465 Planarity : 0.005 0.034 476 Dihedral : 6.387 68.965 395 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.03 % Allowed : 19.80 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.44), residues: 369 helix: 1.47 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -0.87 (0.75), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.002 0.001 HIS A 353 PHE 0.012 0.001 PHE A 348 TYR 0.016 0.001 TYR A 422 ARG 0.002 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.273 Fit side-chains REVERT: A 151 LEU cc_start: 0.8008 (mt) cc_final: 0.7734 (mp) REVERT: A 169 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6583 (ttm) REVERT: A 181 SER cc_start: 0.7391 (OUTLIER) cc_final: 0.6582 (p) REVERT: A 233 LEU cc_start: 0.7652 (tt) cc_final: 0.7413 (mt) outliers start: 15 outliers final: 8 residues processed: 52 average time/residue: 0.8275 time to fit residues: 44.7028 Evaluate side-chains 55 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.157475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.137485 restraints weight = 3205.963| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.15 r_work: 0.3559 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2865 Z= 0.262 Angle : 0.627 6.930 3896 Z= 0.312 Chirality : 0.043 0.142 465 Planarity : 0.005 0.035 476 Dihedral : 6.408 69.294 395 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.36 % Allowed : 20.81 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.44), residues: 369 helix: 1.50 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -0.83 (0.74), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.002 0.001 HIS A 353 PHE 0.012 0.001 PHE A 348 TYR 0.016 0.001 TYR A 422 ARG 0.002 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.313 Fit side-chains REVERT: A 151 LEU cc_start: 0.7929 (mt) cc_final: 0.7632 (mp) REVERT: A 169 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6668 (ttm) REVERT: A 181 SER cc_start: 0.7211 (OUTLIER) cc_final: 0.6451 (p) REVERT: A 233 LEU cc_start: 0.7662 (tt) cc_final: 0.7430 (mt) REVERT: A 453 MET cc_start: 0.7650 (mmp) cc_final: 0.7151 (mmp) outliers start: 13 outliers final: 8 residues processed: 52 average time/residue: 0.8146 time to fit residues: 44.0386 Evaluate side-chains 55 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 35 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.0570 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 34 optimal weight: 0.0870 chunk 17 optimal weight: 0.4980 chunk 21 optimal weight: 0.4980 chunk 30 optimal weight: 0.3980 chunk 36 optimal weight: 0.1980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.163074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143414 restraints weight = 3145.270| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.15 r_work: 0.3623 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2865 Z= 0.181 Angle : 0.593 7.482 3896 Z= 0.294 Chirality : 0.041 0.155 465 Planarity : 0.005 0.034 476 Dihedral : 6.372 70.435 395 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.02 % Allowed : 22.48 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.44), residues: 369 helix: 1.69 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -0.85 (0.75), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE A 393 TYR 0.012 0.001 TYR A 422 ARG 0.001 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.298 Fit side-chains REVERT: A 151 LEU cc_start: 0.7924 (mt) cc_final: 0.7656 (mp) REVERT: A 181 SER cc_start: 0.7000 (OUTLIER) cc_final: 0.6231 (p) REVERT: A 453 MET cc_start: 0.7554 (mmp) cc_final: 0.7121 (mmp) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.8143 time to fit residues: 46.5684 Evaluate side-chains 55 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.0570 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.157753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137647 restraints weight = 3166.126| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.13 r_work: 0.3559 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2865 Z= 0.247 Angle : 0.631 8.190 3896 Z= 0.313 Chirality : 0.043 0.185 465 Planarity : 0.005 0.035 476 Dihedral : 6.395 69.852 395 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.68 % Allowed : 23.15 % Favored : 74.16 % 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: 1.93 (0.44), residues: 369 helix: 1.67 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -0.71 (0.75), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.012 0.001 PHE A 348 TYR 0.016 0.001 TYR A 422 ARG 0.001 0.000 ARG A 471 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.310 Fit side-chains REVERT: A 151 LEU cc_start: 0.8055 (mt) cc_final: 0.7789 (mp) REVERT: A 181 SER cc_start: 0.7549 (OUTLIER) cc_final: 0.6758 (p) REVERT: A 312 GLU cc_start: 0.7985 (tt0) cc_final: 0.7724 (tt0) REVERT: A 453 MET cc_start: 0.7555 (mmp) cc_final: 0.7027 (mmp) outliers start: 8 outliers final: 7 residues processed: 53 average time/residue: 0.8260 time to fit residues: 45.5062 Evaluate side-chains 55 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.156645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.136560 restraints weight = 3104.265| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.10 r_work: 0.3559 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2865 Z= 0.276 Angle : 0.650 9.358 3896 Z= 0.322 Chirality : 0.044 0.177 465 Planarity : 0.005 0.035 476 Dihedral : 6.437 69.468 395 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.03 % Allowed : 21.81 % Favored : 74.16 % 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: 1.82 (0.44), residues: 369 helix: 1.59 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -0.74 (0.75), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.023 0.001 PHE A 348 TYR 0.016 0.001 TYR A 422 ARG 0.001 0.000 ARG A 471 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2040.25 seconds wall clock time: 37 minutes 16.90 seconds (2236.90 seconds total)