Starting phenix.real_space_refine on Wed Mar 5 16:37:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x3k_38038/03_2025/8x3k_38038.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x3k_38038/03_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_38038/03_2025/8x3k_38038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x3k_38038/03_2025/8x3k_38038.map" model { file = "/net/cci-nas-00/data/ceres_data/8x3k_38038/03_2025/8x3k_38038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x3k_38038/03_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-5624/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: 2.54, per 1000 atoms: 0.91 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: 0.75 Conformation dependent library (CDL) restraints added in 357.1 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: 0.26 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: 0.75 Time building geometry restraints manager: 0.88 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.150 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- 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 : 0.304 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: 0.8556 time to fit residues: 47.9406 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 : 0.315 ------------------------------------------------------------------------------- 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 = 0.130320 restraints weight = 3193.764| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.09 r_work: 0.3495 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 61.455 397 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 : 0.294 Fit side-chains REVERT: A 151 LEU cc_start: 0.8138 (mt) cc_final: 0.7893 (mp) REVERT: A 181 SER cc_start: 0.7362 (OUTLIER) cc_final: 0.6648 (p) REVERT: A 310 MET cc_start: 0.8294 (mtt) cc_final: 0.8091 (mtp) REVERT: A 453 MET cc_start: 0.7731 (mmp) cc_final: 0.7245 (mmp) outliers start: 12 outliers final: 6 residues processed: 49 average time/residue: 0.8276 time to fit residues: 42.1467 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 : 0.305 ------------------------------------------------------------------------------- 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: 0.6980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.152408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.133536 restraints weight = 3096.159| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.02 r_work: 0.3551 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2865 Z= 0.223 Angle : 0.604 6.734 3896 Z= 0.304 Chirality : 0.041 0.124 465 Planarity : 0.005 0.037 476 Dihedral : 6.388 66.162 395 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.69 % Allowed : 18.46 % 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: 0.84 (0.44), residues: 369 helix: 0.99 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -1.54 (0.68), 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 0.015 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 58 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.300 Fit side-chains REVERT: A 151 LEU cc_start: 0.8145 (mt) cc_final: 0.7904 (mp) REVERT: A 181 SER cc_start: 0.7308 (OUTLIER) cc_final: 0.6577 (p) REVERT: A 233 LEU cc_start: 0.7949 (tt) cc_final: 0.7715 (tp) REVERT: A 453 MET cc_start: 0.7685 (mmp) cc_final: 0.7291 (mmp) outliers start: 11 outliers final: 5 residues processed: 51 average time/residue: 0.8506 time to fit residues: 45.0532 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 : 0.287 ------------------------------------------------------------------------------- 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 366 ILE Chi-restraints excluded: chain A residue 415 VAL 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: 0.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.150515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.131236 restraints weight = 3268.900| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.11 r_work: 0.3532 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1717 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= 0.265 Angle : 0.623 6.867 3896 Z= 0.310 Chirality : 0.042 0.127 465 Planarity : 0.005 0.034 476 Dihedral : 6.418 67.442 395 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 5.37 % Allowed : 18.79 % Favored : 75.84 % 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: 1.07 (0.44), residues: 369 helix: 1.13 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -1.33 (0.68), 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 353 PHE 0.012 0.001 PHE A 238 TYR 0.016 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 59 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.291 Fit side-chains REVERT: A 151 LEU cc_start: 0.8067 (mt) cc_final: 0.7797 (mp) REVERT: A 181 SER cc_start: 0.7158 (OUTLIER) cc_final: 0.6369 (p) REVERT: A 233 LEU cc_start: 0.7767 (tt) cc_final: 0.7551 (tp) REVERT: A 453 MET cc_start: 0.7664 (mmp) cc_final: 0.7191 (mmp) outliers start: 16 outliers final: 8 residues processed: 49 average time/residue: 0.8712 time to fit residues: 44.4082 Evaluate side-chains 52 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 166 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.157033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136755 restraints weight = 3204.887| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.17 r_work: 0.3546 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1849 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= 0.239 Angle : 0.604 6.830 3896 Z= 0.301 Chirality : 0.041 0.126 465 Planarity : 0.005 0.033 476 Dihedral : 6.460 69.406 395 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.70 % Allowed : 18.46 % Favored : 75.84 % 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: 1.39 (0.44), residues: 369 helix: 1.31 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -1.00 (0.72), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.013 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 63 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.312 Fit side-chains REVERT: A 151 LEU cc_start: 0.8006 (mt) cc_final: 0.7736 (mp) REVERT: A 169 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6668 (ttm) REVERT: A 181 SER cc_start: 0.7197 (OUTLIER) cc_final: 0.6440 (p) REVERT: A 233 LEU cc_start: 0.7717 (tt) cc_final: 0.7460 (mt) REVERT: A 397 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7843 (mtm) REVERT: A 453 MET cc_start: 0.7635 (mmp) cc_final: 0.7162 (mmp) outliers start: 17 outliers final: 9 residues processed: 53 average time/residue: 0.7829 time to fit residues: 43.1369 Evaluate side-chains 56 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 347 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 397 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.151500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132304 restraints weight = 3271.416| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.10 r_work: 0.3550 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2865 Z= 0.244 Angle : 0.612 6.833 3896 Z= 0.306 Chirality : 0.042 0.157 465 Planarity : 0.005 0.033 476 Dihedral : 6.519 70.679 395 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.03 % Allowed : 19.46 % 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: 1.49 (0.44), residues: 369 helix: 1.37 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -0.93 (0.74), 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 353 PHE 0.012 0.001 PHE A 348 TYR 0.016 0.001 TYR A 422 ARG 0.001 0.000 ARG A 357 *********************** 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 60 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.290 Fit side-chains REVERT: A 151 LEU cc_start: 0.8016 (mt) cc_final: 0.7744 (mp) REVERT: A 169 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6749 (ttm) REVERT: A 181 SER cc_start: 0.7260 (OUTLIER) cc_final: 0.6501 (p) REVERT: A 233 LEU cc_start: 0.7748 (tt) cc_final: 0.7498 (mt) REVERT: A 453 MET cc_start: 0.7679 (mmp) cc_final: 0.7195 (mmp) outliers start: 15 outliers final: 8 residues processed: 51 average time/residue: 0.7903 time to fit residues: 41.9345 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 : 0.293 ------------------------------------------------------------------------------- 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 347 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.157299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.136821 restraints weight = 3231.228| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.18 r_work: 0.3570 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2052 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= 0.220 Angle : 0.601 6.796 3896 Z= 0.301 Chirality : 0.042 0.150 465 Planarity : 0.005 0.034 476 Dihedral : 6.494 70.810 395 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.03 % Allowed : 20.13 % Favored : 75.84 % 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: 1.71 (0.44), residues: 369 helix: 1.52 (0.30), residues: 312 sheet: None (None), residues: 0 loop : -0.82 (0.75), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.012 0.001 PHE A 348 TYR 0.015 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 56 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.291 Fit side-chains REVERT: A 151 LEU cc_start: 0.7990 (mt) cc_final: 0.7716 (mp) REVERT: A 169 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6598 (ttm) REVERT: A 233 LEU cc_start: 0.7668 (tt) cc_final: 0.7435 (mt) REVERT: A 397 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7653 (mtm) REVERT: A 453 MET cc_start: 0.7526 (mmp) cc_final: 0.6999 (mmp) outliers start: 12 outliers final: 6 residues processed: 48 average time/residue: 0.8607 time to fit residues: 42.9365 Evaluate side-chains 52 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET 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 397 MET 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: 3.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 0.0980 chunk 13 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.152511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.133680 restraints weight = 3224.989| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.06 r_work: 0.3551 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2112 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= 0.237 Angle : 0.617 6.835 3896 Z= 0.307 Chirality : 0.042 0.141 465 Planarity : 0.005 0.034 476 Dihedral : 6.471 70.353 395 Min Nonbonded Distance : 2.610 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: 1.77 (0.44), residues: 369 helix: 1.57 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -0.85 (0.74), residues: 58 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 : 0.298 Fit side-chains REVERT: A 151 LEU cc_start: 0.8026 (mt) cc_final: 0.7760 (mp) REVERT: A 169 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6841 (ttm) REVERT: A 181 SER cc_start: 0.7383 (OUTLIER) cc_final: 0.6620 (p) REVERT: A 233 LEU cc_start: 0.7781 (tt) cc_final: 0.7554 (mt) REVERT: A 397 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7846 (mtm) REVERT: A 453 MET cc_start: 0.7729 (mmp) cc_final: 0.7230 (mmp) outliers start: 13 outliers final: 8 residues processed: 50 average time/residue: 0.8015 time to fit residues: 41.6633 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 : 0.260 ------------------------------------------------------------------------------- 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 230 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 397 MET 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: 0.7980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.152600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133727 restraints weight = 3203.504| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.05 r_work: 0.3571 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2865 Z= 0.247 Angle : 0.627 7.603 3896 Z= 0.312 Chirality : 0.043 0.168 465 Planarity : 0.005 0.035 476 Dihedral : 6.466 70.115 395 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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: 1.78 (0.44), residues: 369 helix: 1.58 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -0.85 (0.74), 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 353 PHE 0.013 0.001 PHE A 348 TYR 0.016 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 58 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.232 Fit side-chains REVERT: A 151 LEU cc_start: 0.7970 (mt) cc_final: 0.7681 (mp) REVERT: A 169 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6749 (ttm) REVERT: A 181 SER cc_start: 0.7378 (OUTLIER) cc_final: 0.6647 (p) REVERT: A 233 LEU cc_start: 0.7740 (tt) cc_final: 0.7514 (mt) REVERT: A 453 MET cc_start: 0.7689 (mmp) cc_final: 0.7182 (mmp) outliers start: 13 outliers final: 10 residues processed: 52 average time/residue: 0.8588 time to fit residues: 46.3517 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 : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU 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 191 LEU 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 397 MET 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: 1.9990 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.160262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.140461 restraints weight = 3187.822| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.15 r_work: 0.3597 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2865 Z= 0.211 Angle : 0.612 7.583 3896 Z= 0.305 Chirality : 0.042 0.166 465 Planarity : 0.005 0.035 476 Dihedral : 6.621 73.244 395 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.69 % Allowed : 21.48 % 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: 1.88 (0.44), residues: 369 helix: 1.65 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -0.83 (0.74), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.001 0.001 HIS A 353 PHE 0.012 0.001 PHE A 393 TYR 0.014 0.001 TYR A 422 ARG 0.002 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 57 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.307 Fit side-chains REVERT: A 151 LEU cc_start: 0.7956 (mt) cc_final: 0.7694 (mp) REVERT: A 169 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6628 (ttm) REVERT: A 233 LEU cc_start: 0.7634 (tt) cc_final: 0.7423 (mt) REVERT: A 397 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7706 (mtm) REVERT: A 415 VAL cc_start: 0.8596 (t) cc_final: 0.8328 (p) REVERT: A 453 MET cc_start: 0.7619 (mmp) cc_final: 0.7117 (mmp) outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 0.9611 time to fit residues: 50.8197 Evaluate side-chains 53 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 191 LEU 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 397 MET 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: 0.6980 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 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 = 0.3923 r_free = 0.3923 target = 0.156120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135787 restraints weight = 3102.682| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.11 r_work: 0.3540 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2865 Z= 0.270 Angle : 0.643 8.497 3896 Z= 0.320 Chirality : 0.043 0.154 465 Planarity : 0.005 0.035 476 Dihedral : 6.698 73.358 395 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.36 % Allowed : 22.15 % 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: 1.78 (0.44), residues: 369 helix: 1.57 (0.30), residues: 311 sheet: None (None), residues: 0 loop : -0.76 (0.75), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 318 HIS 0.002 0.001 HIS A 353 PHE 0.013 0.001 PHE A 348 TYR 0.017 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: 2070.97 seconds wall clock time: 36 minutes 9.68 seconds (2169.68 seconds total)