Starting phenix.real_space_refine on Wed Mar 5 16:37:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqe_62501/03_2025/9kqe_62501.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqe_62501/03_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_62501/03_2025/9kqe_62501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqe_62501/03_2025/9kqe_62501.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqe_62501/03_2025/9kqe_62501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqe_62501/03_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-5624/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: 2.55, per 1000 atoms: 0.91 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: 0.88 Conformation dependent library (CDL) restraints added in 360.9 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: 0.27 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: 0.75 Time building geometry restraints manager: 0.91 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.270 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.340 ------------------------------------------------------------------------------- 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 : 0.309 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: 0.6101 time to fit residues: 63.6963 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 : 0.297 ------------------------------------------------------------------------------- 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: 2.97 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 : 0.305 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8342 (tt) REVERT: A 179 SER cc_start: 0.7273 (OUTLIER) cc_final: 0.6907 (m) REVERT: A 206 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8167 (ttm) REVERT: A 291 ASP cc_start: 0.8839 (t0) cc_final: 0.8562 (t0) REVERT: A 322 THR cc_start: 0.8459 (m) cc_final: 0.7899 (p) REVERT: A 397 MET cc_start: 0.8464 (ttt) cc_final: 0.8226 (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: 0.6973 time to fit residues: 61.6715 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 : 0.287 ------------------------------------------------------------------------------- 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: 0.4980 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: 0.5980 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.170991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.151843 restraints weight = 3411.984| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.19 r_work: 0.3730 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2700 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= 0.251 Angle : 0.674 8.638 3891 Z= 0.334 Chirality : 0.044 0.134 465 Planarity : 0.005 0.032 476 Dihedral : 5.566 59.593 396 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 6.38 % Allowed : 23.83 % Favored : 69.80 % 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: 0.77 (0.45), residues: 369 helix: 0.97 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -1.83 (0.71), residues: 56 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 0.018 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 85 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 155 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.6654 (mpt-90) REVERT: A 179 SER cc_start: 0.7540 (OUTLIER) cc_final: 0.7058 (m) REVERT: A 291 ASP cc_start: 0.8833 (t0) cc_final: 0.8594 (t70) REVERT: A 322 THR cc_start: 0.8546 (m) cc_final: 0.7954 (p) REVERT: A 397 MET cc_start: 0.8514 (ttt) cc_final: 0.8299 (ttm) REVERT: A 417 VAL cc_start: 0.8449 (t) cc_final: 0.8050 (m) outliers start: 19 outliers final: 11 residues processed: 78 average time/residue: 0.7030 time to fit residues: 57.0873 Evaluate side-chains 75 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 249 THR 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 415 VAL 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: 0.8980 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 27 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 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 = 0.4008 r_free = 0.4008 target = 0.170308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.150937 restraints weight = 3452.808| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.22 r_work: 0.3705 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3063 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= 0.245 Angle : 0.670 8.591 3891 Z= 0.329 Chirality : 0.043 0.129 465 Planarity : 0.005 0.031 476 Dihedral : 5.411 57.531 396 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.70 % Allowed : 27.52 % Favored : 66.78 % 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: 1.13 (0.45), residues: 369 helix: 1.24 (0.31), residues: 311 sheet: None (None), residues: 0 loop : -1.73 (0.69), residues: 58 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 0.022 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 81 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.307 Fit side-chains REVERT: A 155 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6618 (mpt-90) REVERT: A 179 SER cc_start: 0.7566 (OUTLIER) cc_final: 0.7060 (m) REVERT: A 291 ASP cc_start: 0.8813 (t0) cc_final: 0.8566 (t70) REVERT: A 322 THR cc_start: 0.8497 (m) cc_final: 0.7797 (p) REVERT: A 397 MET cc_start: 0.8536 (ttt) cc_final: 0.8316 (ttm) outliers start: 17 outliers final: 8 residues processed: 75 average time/residue: 0.7078 time to fit residues: 55.3567 Evaluate side-chains 69 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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: 0.0570 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.170038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.150656 restraints weight = 3481.156| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.23 r_work: 0.3704 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3218 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= 0.241 Angle : 0.664 9.885 3891 Z= 0.324 Chirality : 0.043 0.128 465 Planarity : 0.005 0.030 476 Dihedral : 5.093 54.398 394 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.37 % Allowed : 26.51 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.45), residues: 369 helix: 1.33 (0.31), residues: 313 sheet: None (None), residues: 0 loop : -1.66 (0.71), residues: 56 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 0.017 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 76 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.286 Fit side-chains REVERT: A 35 MET cc_start: 0.8523 (ttm) cc_final: 0.8253 (ttt) REVERT: A 179 SER cc_start: 0.7506 (OUTLIER) cc_final: 0.7034 (m) REVERT: A 221 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7914 (mtt) REVERT: A 234 VAL cc_start: 0.8647 (p) cc_final: 0.8419 (m) REVERT: A 291 ASP cc_start: 0.8829 (t0) cc_final: 0.8568 (t70) REVERT: A 317 ILE cc_start: 0.8597 (mm) cc_final: 0.8297 (mt) REVERT: A 388 ASN cc_start: 0.8854 (m110) cc_final: 0.8561 (m110) REVERT: A 397 MET cc_start: 0.8543 (ttt) cc_final: 0.8325 (ttm) REVERT: A 468 PHE cc_start: 0.8869 (t80) cc_final: 0.8631 (t80) outliers start: 16 outliers final: 9 residues processed: 71 average time/residue: 0.7460 time to fit residues: 55.1609 Evaluate side-chains 68 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 23 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.171453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.152722 restraints weight = 3536.933| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.12 r_work: 0.3748 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3388 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= 0.221 Angle : 0.668 11.601 3891 Z= 0.321 Chirality : 0.042 0.129 465 Planarity : 0.005 0.029 476 Dihedral : 4.891 48.756 394 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 5.37 % Allowed : 28.19 % 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: 1.52 (0.46), residues: 369 helix: 1.49 (0.31), residues: 313 sheet: None (None), residues: 0 loop : -1.65 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 PHE 0.012 0.001 PHE A 238 TYR 0.017 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 75 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.269 Fit side-chains REVERT: A 179 SER cc_start: 0.7438 (OUTLIER) cc_final: 0.7077 (m) REVERT: A 234 VAL cc_start: 0.8705 (p) cc_final: 0.8485 (m) REVERT: A 291 ASP cc_start: 0.8798 (t0) cc_final: 0.8572 (t70) REVERT: A 317 ILE cc_start: 0.8701 (mm) cc_final: 0.8443 (mt) REVERT: A 388 ASN cc_start: 0.8918 (m110) cc_final: 0.8618 (m110) REVERT: A 397 MET cc_start: 0.8577 (ttt) cc_final: 0.8373 (ttm) REVERT: A 468 PHE cc_start: 0.8852 (t80) cc_final: 0.8637 (t80) outliers start: 16 outliers final: 8 residues processed: 71 average time/residue: 0.7319 time to fit residues: 54.0931 Evaluate side-chains 66 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 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 = 0.4045 r_free = 0.4045 target = 0.173181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.153852 restraints weight = 3523.125| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.25 r_work: 0.3756 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3538 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= 0.262 Angle : 0.678 11.561 3891 Z= 0.327 Chirality : 0.043 0.129 465 Planarity : 0.005 0.029 476 Dihedral : 4.830 46.076 394 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.37 % Allowed : 27.85 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.46), residues: 369 helix: 1.50 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -1.65 (0.73), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.013 0.001 PHE A 238 TYR 0.014 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 78 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.308 Fit side-chains REVERT: A 291 ASP cc_start: 0.8844 (t0) cc_final: 0.8587 (t70) REVERT: A 317 ILE cc_start: 0.8705 (mm) cc_final: 0.8465 (mt) REVERT: A 388 ASN cc_start: 0.8955 (m110) cc_final: 0.8614 (m110) REVERT: A 397 MET cc_start: 0.8551 (ttt) cc_final: 0.8326 (ttm) REVERT: A 417 VAL cc_start: 0.8485 (t) cc_final: 0.8051 (m) outliers start: 16 outliers final: 9 residues processed: 75 average time/residue: 0.7174 time to fit residues: 55.9740 Evaluate side-chains 68 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 11 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 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 = 0.4075 r_free = 0.4075 target = 0.176021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155611 restraints weight = 3390.795| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.25 r_work: 0.3727 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3739 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 : 0.704 12.310 3891 Z= 0.339 Chirality : 0.044 0.150 465 Planarity : 0.005 0.028 476 Dihedral : 4.895 46.830 394 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.03 % Allowed : 29.53 % Favored : 65.44 % 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: 1.51 (0.46), residues: 369 helix: 1.50 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -1.82 (0.73), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 PHE 0.015 0.002 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 76 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.292 Fit side-chains REVERT: A 154 ASN cc_start: 0.8654 (t0) cc_final: 0.8427 (t0) REVERT: A 291 ASP cc_start: 0.8867 (t0) cc_final: 0.8599 (t70) REVERT: A 397 MET cc_start: 0.8569 (ttt) cc_final: 0.8346 (ttm) REVERT: A 417 VAL cc_start: 0.8433 (t) cc_final: 0.8014 (m) outliers start: 15 outliers final: 10 residues processed: 74 average time/residue: 0.7257 time to fit residues: 55.8778 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 : 0.286 ------------------------------------------------------------------------------- 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 191 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 30 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.177350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.157417 restraints weight = 3443.494| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.30 r_work: 0.3770 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2862 Z= 0.205 Angle : 0.688 11.423 3891 Z= 0.329 Chirality : 0.043 0.137 465 Planarity : 0.005 0.030 476 Dihedral : 4.840 45.979 394 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.68 % Allowed : 33.56 % Favored : 63.76 % 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 (0.46), residues: 369 helix: 1.51 (0.31), residues: 315 sheet: None (None), residues: 0 loop : -2.03 (0.72), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 451 HIS 0.001 0.001 HIS A 353 PHE 0.029 0.002 PHE A 468 TYR 0.012 0.002 TYR A 433 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: 8 poor density : 66 time to evaluate : 0.305 Fit side-chains REVERT: A 291 ASP cc_start: 0.8903 (t0) cc_final: 0.8602 (t0) outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.6899 time to fit residues: 53.2400 Evaluate side-chains 64 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 265 ILE Chi-restraints excluded: chain A residue 368 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: 0.8980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.0030 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.174582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.154455 restraints weight = 3405.752| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.25 r_work: 0.3751 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2862 Z= 0.231 Angle : 0.716 12.014 3891 Z= 0.341 Chirality : 0.045 0.133 465 Planarity : 0.005 0.033 476 Dihedral : 4.903 45.731 394 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.68 % Allowed : 36.24 % 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: 1.65 (0.46), residues: 369 helix: 1.60 (0.31), residues: 310 sheet: None (None), residues: 0 loop : -1.55 (0.75), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.035 0.002 PHE A 238 TYR 0.014 0.002 TYR A 422 ARG 0.001 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 67 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.314 Fit side-chains REVERT: A 291 ASP cc_start: 0.8901 (t0) cc_final: 0.8629 (t70) outliers start: 5 outliers final: 5 residues processed: 67 average time/residue: 0.7682 time to fit residues: 53.5339 Evaluate side-chains 65 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 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 368 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: 0.8980 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4058 r_free = 0.4058 target = 0.173930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.153797 restraints weight = 3396.306| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.28 r_work: 0.3743 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2862 Z= 0.234 Angle : 0.739 10.507 3891 Z= 0.344 Chirality : 0.045 0.138 465 Planarity : 0.005 0.035 476 Dihedral : 4.861 45.330 394 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.01 % Allowed : 36.58 % Favored : 61.41 % 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: 1.53 (0.31), residues: 315 sheet: None (None), residues: 0 loop : -1.78 (0.75), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.034 0.002 PHE A 238 TYR 0.014 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: 2058.95 seconds wall clock time: 36 minutes 16.41 seconds (2176.41 seconds total)