Starting phenix.real_space_refine on Mon Feb 10 21:40:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqe_62501/02_2025/9kqe_62501.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqe_62501/02_2025/9kqe_62501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kqe_62501/02_2025/9kqe_62501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqe_62501/02_2025/9kqe_62501.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqe_62501/02_2025/9kqe_62501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqe_62501/02_2025/9kqe_62501.cif" } resolution = 3.0 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= 0.075 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 1863 2.51 5 N 433 2.21 5 O 471 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: 2795 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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.60, per 1000 atoms: 0.93 Number of scatterers: 2795 At special positions: 0 Unit cell: (68.036, 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 471 8.00 N 433 7.00 C 1863 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: 0.81 Conformation dependent library (CDL) restraints added in 362.4 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 91.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 18 through 44 removed outlier: 3.916A pdb=" N ILE A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 133 through 157 removed outlier: 4.443A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 4.132A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.942A 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: 3.530A 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: 3.780A pdb=" N ASN A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.543A 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: 4.068A 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: 3.798A 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: 4.879A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.352A 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: 3.991A 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: 0.68 Time building geometry restraints manager: 0.90 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: 558 1.33 - 1.45: 618 1.45 - 1.57: 1638 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 2862 Sorted by residual: bond pdb=" CA SER A 197 " pdb=" C SER A 197 " ideal model delta sigma weight residual 1.524 1.487 0.037 1.27e-02 6.20e+03 8.31e+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 5.97e+00 bond pdb=" C ILE A 301 " pdb=" O ILE A 301 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.17e-02 7.31e+03 5.74e+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 5.22e+00 bond pdb=" CA ASP A 291 " pdb=" C ASP A 291 " ideal model delta sigma weight residual 1.524 1.502 0.022 1.08e-02 8.57e+03 4.07e+00 ... (remaining 2857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 3619 1.42 - 2.84: 203 2.84 - 4.25: 42 4.25 - 5.67: 21 5.67 - 7.09: 6 Bond angle restraints: 3891 Sorted by residual: angle pdb=" CA ILE A 44 " pdb=" C ILE A 44 " pdb=" N PRO A 45 " ideal model delta sigma weight residual 120.83 117.47 3.36 5.90e-01 2.87e+00 3.24e+01 angle pdb=" C ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta sigma weight residual 113.70 108.57 5.13 9.50e-01 1.11e+00 2.92e+01 angle pdb=" N VAL A 427 " pdb=" CA VAL A 427 " pdb=" C VAL A 427 " ideal model delta sigma weight residual 111.00 106.05 4.95 1.09e+00 8.42e-01 2.06e+01 angle pdb=" N ARG A 274 " pdb=" CA ARG A 274 " pdb=" C ARG A 274 " ideal model delta sigma weight residual 109.95 116.90 -6.95 1.59e+00 3.96e-01 1.91e+01 angle pdb=" N VAL A 417 " pdb=" CA VAL A 417 " pdb=" C VAL A 417 " ideal model delta sigma weight residual 108.12 102.17 5.95 1.44e+00 4.82e-01 1.71e+01 ... (remaining 3886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.77: 1442 12.77 - 25.53: 156 25.53 - 38.30: 53 38.30 - 51.07: 19 51.07 - 63.83: 6 Dihedral angle restraints: 1676 sinusoidal: 624 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 180.00 163.34 16.66 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 -176.17 -63.83 2 2.00e+01 2.50e-03 9.67e+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 -82.90 52.90 1 2.00e+01 2.50e-03 9.52e+00 ... (remaining 1673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 255 0.030 - 0.061: 133 0.061 - 0.091: 47 0.091 - 0.121: 23 0.121 - 0.152: 7 Chirality restraints: 465 Sorted by residual: 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 5.76e-01 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 2.58 0.14 2.00e-01 2.50e+01 4.97e-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 4.54e-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 1.77e-02 3.15e+00 pdb=" C ALA A 164 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA A 164 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY A 165 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO A 236 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " -0.021 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 1.44e-02 2.07e+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 " -0.008 2.00e-02 2.50e+03 ... (remaining 473 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 637 2.77 - 3.30: 2790 3.30 - 3.83: 4758 3.83 - 4.37: 5520 4.37 - 4.90: 9703 Nonbonded interactions: 23408 Sorted by model distance: nonbonded pdb=" O ILE A 301 " pdb=" ND2 ASN A 305 " model vdw 2.237 3.120 nonbonded pdb=" O THR A 212 " pdb=" OG1 THR A 212 " model vdw 2.324 3.040 nonbonded pdb=" O PRO A 336 " pdb=" OG SER A 340 " model vdw 2.417 3.040 nonbonded pdb=" NH2 ARG A 19 " pdb=" OE1 GLU A 216 " model vdw 2.466 3.120 nonbonded pdb=" OE1 GLU A 215 " pdb=" ND1 HIS A 353 " model vdw 2.481 3.120 ... (remaining 23403 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: 0.750 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: 0.030 Process input model: 12.260 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 0.059 2862 Z= 0.476 Angle : 0.868 7.088 3891 Z= 0.532 Chirality : 0.046 0.152 465 Planarity : 0.005 0.037 476 Dihedral : 13.458 63.834 1006 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.68 % Allowed : 14.09 % Favored : 84.23 % 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: -2.23 (0.39), residues: 369 helix: -1.07 (0.27), residues: 297 sheet: None (None), residues: 0 loop : -2.52 (0.61), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.004 0.001 HIS A 353 PHE 0.014 0.002 PHE A 348 TYR 0.019 0.002 TYR A 422 ARG 0.002 0.001 ARG A 413 *********************** 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 101 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.281 Fit side-chains REVERT: A 322 THR cc_start: 0.8357 (m) cc_final: 0.8087 (p) REVERT: A 397 MET cc_start: 0.8037 (ttt) cc_final: 0.7697 (ttm) outliers start: 5 outliers final: 3 residues processed: 100 average time/residue: 0.6486 time to fit residues: 67.6624 Evaluate side-chains 72 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE 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: 1.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.171784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.153312 restraints weight = 3392.541| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.19 r_work: 0.3725 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2862 Z= 0.288 Angle : 0.697 6.780 3891 Z= 0.349 Chirality : 0.044 0.135 465 Planarity : 0.005 0.034 476 Dihedral : 5.989 52.132 398 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 6.04 % Allowed : 21.81 % Favored : 72.15 % 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: -0.07 (0.42), residues: 369 helix: 0.40 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -2.07 (0.70), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.018 0.002 PHE A 468 TYR 0.015 0.002 TYR A 422 ARG 0.002 0.000 ARG A 471 *********************** 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 92 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8343 (tt) REVERT: A 179 SER cc_start: 0.7273 (OUTLIER) cc_final: 0.6906 (m) REVERT: A 206 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8168 (ttm) REVERT: A 291 ASP cc_start: 0.8839 (t0) cc_final: 0.8562 (t0) REVERT: A 322 THR cc_start: 0.8460 (m) cc_final: 0.7900 (p) REVERT: A 397 MET cc_start: 0.8464 (ttt) cc_final: 0.8227 (ttm) REVERT: A 417 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8059 (m) outliers start: 18 outliers final: 8 residues processed: 85 average time/residue: 0.7166 time to fit residues: 63.4069 Evaluate side-chains 78 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.171365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.152276 restraints weight = 3414.203| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.19 r_work: 0.3734 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2862 Z= 0.246 Angle : 0.670 8.581 3891 Z= 0.332 Chirality : 0.043 0.138 465 Planarity : 0.005 0.032 476 Dihedral : 5.536 59.271 396 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.70 % Allowed : 25.50 % Favored : 68.79 % 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 (0.45), residues: 369 helix: 1.00 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -1.69 (0.71), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.012 0.001 PHE A 238 TYR 0.017 0.002 TYR A 422 ARG 0.004 0.001 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 84 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 155 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.6693 (mpt-90) REVERT: A 179 SER cc_start: 0.7582 (OUTLIER) cc_final: 0.7027 (m) REVERT: A 291 ASP cc_start: 0.8833 (t0) cc_final: 0.8593 (t70) REVERT: A 322 THR cc_start: 0.8533 (m) cc_final: 0.7894 (p) REVERT: A 397 MET cc_start: 0.8506 (ttt) cc_final: 0.8299 (ttm) REVERT: A 417 VAL cc_start: 0.8432 (t) cc_final: 0.8033 (m) outliers start: 17 outliers final: 9 residues processed: 78 average time/residue: 0.7538 time to fit residues: 61.1401 Evaluate side-chains 72 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 468 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.169629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.150348 restraints weight = 3461.908| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.21 r_work: 0.3692 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2862 Z= 0.264 Angle : 0.678 8.411 3891 Z= 0.333 Chirality : 0.043 0.131 465 Planarity : 0.005 0.030 476 Dihedral : 5.397 56.947 396 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 5.70 % Allowed : 27.85 % Favored : 66.44 % 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: 1.12 (0.45), residues: 369 helix: 1.19 (0.31), residues: 313 sheet: None (None), residues: 0 loop : -1.58 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.017 0.001 PHE A 468 TYR 0.016 0.002 TYR A 422 ARG 0.002 0.000 ARG A 217 *********************** 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 80 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.305 Fit side-chains REVERT: A 155 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.6691 (mpt-90) REVERT: A 179 SER cc_start: 0.7615 (OUTLIER) cc_final: 0.7096 (m) REVERT: A 291 ASP cc_start: 0.8840 (t0) cc_final: 0.8604 (t70) REVERT: A 322 THR cc_start: 0.8521 (m) cc_final: 0.7821 (p) REVERT: A 397 MET cc_start: 0.8551 (ttt) cc_final: 0.8318 (ttm) REVERT: A 417 VAL cc_start: 0.8444 (t) cc_final: 0.8034 (m) outliers start: 17 outliers final: 8 residues processed: 75 average time/residue: 0.7811 time to fit residues: 60.8849 Evaluate side-chains 68 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 405 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 23 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 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 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.170434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.151407 restraints weight = 3478.665| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.11 r_work: 0.3734 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2862 Z= 0.232 Angle : 0.661 9.460 3891 Z= 0.324 Chirality : 0.043 0.128 465 Planarity : 0.005 0.029 476 Dihedral : 5.115 55.137 394 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 5.37 % Allowed : 27.18 % Favored : 67.45 % 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: 1.25 (0.45), residues: 369 helix: 1.29 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -1.68 (0.73), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.013 0.001 PHE A 238 TYR 0.018 0.002 TYR A 422 ARG 0.002 0.000 ARG A 217 *********************** 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 78 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.309 Fit side-chains REVERT: A 35 MET cc_start: 0.8633 (ttm) cc_final: 0.8353 (ttt) REVERT: A 179 SER cc_start: 0.7548 (OUTLIER) cc_final: 0.7097 (m) REVERT: A 221 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8074 (mtt) REVERT: A 291 ASP cc_start: 0.8945 (t0) cc_final: 0.8700 (t70) REVERT: A 317 ILE cc_start: 0.8700 (mm) cc_final: 0.8387 (mt) REVERT: A 388 ASN cc_start: 0.8908 (m110) cc_final: 0.8611 (m110) REVERT: A 468 PHE cc_start: 0.8927 (t80) cc_final: 0.8678 (t80) outliers start: 16 outliers final: 8 residues processed: 73 average time/residue: 0.7395 time to fit residues: 56.2071 Evaluate side-chains 68 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 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 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 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 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.168488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.148922 restraints weight = 3531.997| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.27 r_work: 0.3706 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2862 Z= 0.265 Angle : 0.692 11.428 3891 Z= 0.333 Chirality : 0.043 0.132 465 Planarity : 0.004 0.029 476 Dihedral : 5.050 52.938 394 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 6.04 % Allowed : 27.52 % Favored : 66.44 % 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: 1.36 (0.45), residues: 369 helix: 1.38 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -1.75 (0.73), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.015 0.001 PHE A 348 TYR 0.019 0.002 TYR A 422 ARG 0.002 0.000 ARG A 217 *********************** 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 79 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.282 Fit side-chains REVERT: A 179 SER cc_start: 0.7474 (OUTLIER) cc_final: 0.7098 (m) REVERT: A 291 ASP cc_start: 0.8837 (t0) cc_final: 0.8603 (t70) REVERT: A 317 ILE cc_start: 0.8675 (mm) cc_final: 0.8396 (mt) REVERT: A 388 ASN cc_start: 0.8932 (m110) cc_final: 0.8591 (m110) REVERT: A 417 VAL cc_start: 0.8434 (t) cc_final: 0.8070 (m) REVERT: A 468 PHE cc_start: 0.8861 (t80) cc_final: 0.8629 (t80) outliers start: 18 outliers final: 9 residues processed: 74 average time/residue: 0.7252 time to fit residues: 55.8805 Evaluate side-chains 68 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 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 36 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.168093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.149017 restraints weight = 3567.575| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.15 r_work: 0.3705 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2862 Z= 0.278 Angle : 0.713 11.653 3891 Z= 0.340 Chirality : 0.044 0.133 465 Planarity : 0.005 0.030 476 Dihedral : 4.964 49.984 394 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.70 % Allowed : 29.53 % Favored : 64.77 % 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: 1.38 (0.45), residues: 369 helix: 1.39 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -1.71 (0.73), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.012 0.001 PHE A 238 TYR 0.018 0.002 TYR A 422 ARG 0.002 0.000 ARG A 357 *********************** 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 80 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.262 Fit side-chains REVERT: A 179 SER cc_start: 0.7443 (OUTLIER) cc_final: 0.7176 (m) REVERT: A 291 ASP cc_start: 0.8796 (t0) cc_final: 0.8577 (t70) REVERT: A 317 ILE cc_start: 0.8706 (mm) cc_final: 0.8452 (mt) REVERT: A 388 ASN cc_start: 0.8940 (m110) cc_final: 0.8605 (m110) REVERT: A 417 VAL cc_start: 0.8474 (t) cc_final: 0.8081 (m) REVERT: A 468 PHE cc_start: 0.8872 (t80) cc_final: 0.8659 (t80) outliers start: 17 outliers final: 9 residues processed: 77 average time/residue: 0.7214 time to fit residues: 57.7897 Evaluate side-chains 71 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 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 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.170619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.151113 restraints weight = 3429.823| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.24 r_work: 0.3731 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2862 Z= 0.228 Angle : 0.695 10.864 3891 Z= 0.330 Chirality : 0.043 0.130 465 Planarity : 0.004 0.029 476 Dihedral : 4.865 47.424 394 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 5.70 % Allowed : 29.53 % Favored : 64.77 % 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: 1.46 (0.46), residues: 369 helix: 1.46 (0.31), residues: 315 sheet: None (None), residues: 0 loop : -1.85 (0.72), residues: 54 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 0.015 0.001 PHE A 166 TYR 0.016 0.002 TYR A 422 ARG 0.002 0.000 ARG A 357 *********************** 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 89 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.337 Fit side-chains REVERT: A 291 ASP cc_start: 0.8887 (t0) cc_final: 0.8618 (t70) REVERT: A 317 ILE cc_start: 0.8677 (mm) cc_final: 0.8439 (mt) REVERT: A 417 VAL cc_start: 0.8407 (t) cc_final: 0.8007 (m) outliers start: 17 outliers final: 11 residues processed: 86 average time/residue: 0.6709 time to fit residues: 60.2471 Evaluate side-chains 73 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 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 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.0770 chunk 30 optimal weight: 0.0770 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.174525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.154405 restraints weight = 3444.747| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.26 r_work: 0.3752 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2862 Z= 0.223 Angle : 0.714 11.417 3891 Z= 0.336 Chirality : 0.044 0.148 465 Planarity : 0.005 0.030 476 Dihedral : 4.813 46.116 394 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.03 % Allowed : 33.89 % Favored : 62.08 % 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: 1.48 (0.46), residues: 369 helix: 1.47 (0.31), residues: 315 sheet: None (None), residues: 0 loop : -1.84 (0.74), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.001 0.001 HIS A 353 PHE 0.018 0.001 PHE A 238 TYR 0.016 0.002 TYR A 422 ARG 0.002 0.000 ARG A 357 *********************** 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 74 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.286 Fit side-chains REVERT: A 291 ASP cc_start: 0.8909 (t0) cc_final: 0.8636 (t70) REVERT: A 317 ILE cc_start: 0.8653 (mm) cc_final: 0.8431 (mt) REVERT: A 355 MET cc_start: 0.8778 (ttp) cc_final: 0.8551 (ttm) REVERT: A 388 ASN cc_start: 0.8882 (m110) cc_final: 0.8668 (m110) REVERT: A 417 VAL cc_start: 0.8368 (t) cc_final: 0.7957 (m) outliers start: 12 outliers final: 10 residues processed: 73 average time/residue: 0.7422 time to fit residues: 56.4206 Evaluate side-chains 72 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 472 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 5 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.173643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.153987 restraints weight = 3411.676| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.24 r_work: 0.3770 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2862 Z= 0.214 Angle : 0.724 11.734 3891 Z= 0.336 Chirality : 0.044 0.140 465 Planarity : 0.005 0.033 476 Dihedral : 4.796 46.063 394 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.03 % Allowed : 33.89 % Favored : 62.08 % 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: 1.56 (0.46), residues: 369 helix: 1.55 (0.31), residues: 315 sheet: None (None), residues: 0 loop : -2.01 (0.72), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.001 0.000 HIS A 353 PHE 0.018 0.001 PHE A 166 TYR 0.016 0.002 TYR A 422 ARG 0.002 0.000 ARG A 357 ********************** 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 77 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.295 Fit side-chains REVERT: A 291 ASP cc_start: 0.8909 (t0) cc_final: 0.8629 (t70) REVERT: A 317 ILE cc_start: 0.8627 (mm) cc_final: 0.8419 (mt) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.7224 time to fit residues: 55.6432 Evaluate side-chains 71 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 472 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.177220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.156928 restraints weight = 3371.216| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.27 r_work: 0.3777 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2862 Z= 0.209 Angle : 0.744 11.756 3891 Z= 0.340 Chirality : 0.044 0.140 465 Planarity : 0.005 0.036 476 Dihedral : 4.834 45.118 394 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.03 % Allowed : 34.90 % Favored : 61.07 % 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: 1.57 (0.46), residues: 369 helix: 1.57 (0.31), residues: 315 sheet: None (None), residues: 0 loop : -2.03 (0.73), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.000 0.000 HIS A 353 PHE 0.017 0.001 PHE A 238 TYR 0.015 0.002 TYR A 422 ARG 0.002 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2008.53 seconds wall clock time: 36 minutes 26.16 seconds (2186.16 seconds total)