Starting phenix.real_space_refine on Sun Mar 10 17:38:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/03_2024/8sib_40505.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/03_2024/8sib_40505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/03_2024/8sib_40505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/03_2024/8sib_40505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/03_2024/8sib_40505.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sib_40505/03_2024/8sib_40505.pdb" } resolution = 2.62 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= 0.000 sd= 0.017 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 18 5.16 5 C 2261 2.51 5 N 619 2.21 5 O 646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 151": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3544 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3544 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 2.48, per 1000 atoms: 0.70 Number of scatterers: 3544 At special positions: 0 Unit cell: (66.4, 94.62, 74.7, 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 18 16.00 O 646 8.00 N 619 7.00 C 2261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 44 " distance=2.04 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 36 " distance=2.04 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 44 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.27 Conformation dependent library (CDL) restraints added in 743.8 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 840 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 38.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 116 through 125 removed outlier: 3.534A pdb=" N LEU A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 167 removed outlier: 3.511A pdb=" N LEU A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 removed outlier: 4.447A pdb=" N HIS A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 258 through 273 removed outlier: 4.302A pdb=" N LEU A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.755A pdb=" N GLN A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 removed outlier: 3.624A pdb=" N GLN A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.832A pdb=" N THR A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 390 through 398 removed outlier: 3.538A pdb=" N ALA A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 418 Processing helix chain 'A' and resid 419 through 426 removed outlier: 3.943A pdb=" N ALA A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 449 removed outlier: 3.507A pdb=" N LEU A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.823A pdb=" N GLU A 15 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 94 removed outlier: 6.479A pdb=" N LYS A 107 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU A 247 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL A 109 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASP A 249 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU A 111 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR A 201 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE A 246 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY A 203 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 248 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA A 205 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N CYS A 200 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 135 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU A 172 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 137 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 312 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE A 381 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 314 " --> pdb=" O PHE A 381 " (cutoff:3.500A) 117 hydrogen bonds defined for protein. 342 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: 0.89 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1156 1.34 - 1.47: 780 1.47 - 1.59: 1652 1.59 - 1.71: 0 1.71 - 1.83: 26 Bond restraints: 3614 Sorted by residual: bond pdb=" C GLU A 343 " pdb=" N PRO A 344 " ideal model delta sigma weight residual 1.336 1.370 -0.034 1.25e-02 6.40e+03 7.38e+00 bond pdb=" N SER A 101 " pdb=" CA SER A 101 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.16e+00 bond pdb=" C LEU A 30 " pdb=" N PRO A 31 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.04e+00 bond pdb=" C SER A 307 " pdb=" N PRO A 308 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.18e-02 7.18e+03 4.02e+00 bond pdb=" CB ILE A 412 " pdb=" CG2 ILE A 412 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.36e+00 ... (remaining 3609 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.42: 108 106.42 - 113.30: 2007 113.30 - 120.18: 1265 120.18 - 127.07: 1458 127.07 - 133.95: 58 Bond angle restraints: 4896 Sorted by residual: angle pdb=" C ARG A 46 " pdb=" N LEU A 47 " pdb=" CA LEU A 47 " ideal model delta sigma weight residual 121.54 133.47 -11.93 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C GLU A 76 " pdb=" N GLU A 77 " pdb=" CA GLU A 77 " ideal model delta sigma weight residual 122.46 129.98 -7.52 1.41e+00 5.03e-01 2.84e+01 angle pdb=" C CYS A 36 " pdb=" N GLN A 37 " pdb=" CA GLN A 37 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C VAL A 48 " pdb=" N LYS A 49 " pdb=" CA LYS A 49 " ideal model delta sigma weight residual 121.54 130.64 -9.10 1.91e+00 2.74e-01 2.27e+01 angle pdb=" C GLY A 100 " pdb=" N SER A 101 " pdb=" CA SER A 101 " ideal model delta sigma weight residual 121.54 130.39 -8.85 1.91e+00 2.74e-01 2.15e+01 ... (remaining 4891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 2018 15.41 - 30.83: 117 30.83 - 46.24: 29 46.24 - 61.66: 8 61.66 - 77.07: 7 Dihedral angle restraints: 2179 sinusoidal: 877 harmonic: 1302 Sorted by residual: dihedral pdb=" CA SER A 307 " pdb=" C SER A 307 " pdb=" N PRO A 308 " pdb=" CA PRO A 308 " ideal model delta harmonic sigma weight residual -180.00 -123.29 -56.71 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA LEU A 30 " pdb=" C LEU A 30 " pdb=" N PRO A 31 " pdb=" CA PRO A 31 " ideal model delta harmonic sigma weight residual -180.00 -126.99 -53.01 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ILE A 383 " pdb=" C ILE A 383 " pdb=" N GLY A 384 " pdb=" CA GLY A 384 " ideal model delta harmonic sigma weight residual -180.00 -131.62 -48.38 0 5.00e+00 4.00e-02 9.36e+01 ... (remaining 2176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 438 0.065 - 0.130: 103 0.130 - 0.195: 19 0.195 - 0.260: 1 0.260 - 0.325: 5 Chirality restraints: 566 Sorted by residual: chirality pdb=" CB VAL A 176 " pdb=" CA VAL A 176 " pdb=" CG1 VAL A 176 " pdb=" CG2 VAL A 176 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CG LEU A 47 " pdb=" CB LEU A 47 " pdb=" CD1 LEU A 47 " pdb=" CD2 LEU A 47 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE A 383 " pdb=" CA ILE A 383 " pdb=" CG1 ILE A 383 " pdb=" CG2 ILE A 383 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 563 not shown) Planarity restraints: 622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 95 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE A 95 " -0.062 2.00e-02 2.50e+03 pdb=" O ILE A 95 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN A 96 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 30 " -0.058 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO A 31 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 31 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C PRO A 31 " 0.055 2.00e-02 2.50e+03 pdb=" O PRO A 31 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY A 32 " -0.018 2.00e-02 2.50e+03 ... (remaining 619 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 836 2.79 - 3.32: 3127 3.32 - 3.85: 5541 3.85 - 4.37: 6449 4.37 - 4.90: 11243 Nonbonded interactions: 27196 Sorted by model distance: nonbonded pdb=" O PHE A 290 " pdb=" OG1 THR A 318 " model vdw 2.265 2.440 nonbonded pdb=" O ALA A 163 " pdb=" OG1 THR A 167 " model vdw 2.324 2.440 nonbonded pdb=" OH TYR A 108 " pdb=" O LEU A 216 " model vdw 2.338 2.440 nonbonded pdb=" NH1 ARG A 41 " pdb=" O ARG A 46 " model vdw 2.348 2.520 nonbonded pdb=" N LEU A 30 " pdb=" O LEU A 30 " model vdw 2.374 2.496 ... (remaining 27191 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.660 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.420 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 : 0.007 0.060 3614 Z= 0.439 Angle : 1.304 13.305 4896 Z= 0.754 Chirality : 0.064 0.325 566 Planarity : 0.008 0.088 622 Dihedral : 11.699 75.711 1330 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 1.33 % Allowed : 12.89 % Favored : 85.78 % Rotamer: Outliers : 0.78 % Allowed : 3.88 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 17.65 % Twisted General : 0.92 % 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: -5.28 (0.28), residues: 450 helix: -4.12 (0.18), residues: 167 sheet: -1.75 (0.55), residues: 62 loop : -3.55 (0.33), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 6 HIS 0.012 0.002 HIS A 242 PHE 0.021 0.004 PHE A 381 TYR 0.028 0.003 TYR A 108 ARG 0.007 0.001 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 102 HIS cc_start: 0.7321 (m-70) cc_final: 0.6998 (m170) REVERT: A 198 LYS cc_start: 0.8504 (mmtt) cc_final: 0.7943 (ttpp) REVERT: A 211 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7185 (mm-30) REVERT: A 352 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8615 (mttp) REVERT: A 370 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8435 (mm-30) outliers start: 3 outliers final: 1 residues processed: 80 average time/residue: 1.2930 time to fit residues: 106.3056 Evaluate side-chains 43 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.0270 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 86 GLN A 144 GLN A 154 GLN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS A 404 ASN A 432 GLN A 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3614 Z= 0.242 Angle : 0.793 11.268 4896 Z= 0.403 Chirality : 0.047 0.241 566 Planarity : 0.006 0.076 622 Dihedral : 7.446 38.936 483 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.89 % Allowed : 13.56 % Favored : 85.56 % Rotamer: Outliers : 3.62 % Allowed : 12.66 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.69 % 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: -3.45 (0.33), residues: 450 helix: -1.40 (0.34), residues: 172 sheet: -1.99 (0.60), residues: 49 loop : -3.15 (0.34), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 6 HIS 0.006 0.001 HIS A 51 PHE 0.010 0.001 PHE A 146 TYR 0.009 0.001 TYR A 327 ARG 0.007 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 37 GLN cc_start: 0.6484 (OUTLIER) cc_final: 0.6240 (mm-40) REVERT: A 198 LYS cc_start: 0.8490 (mmtt) cc_final: 0.8269 (tttt) REVERT: A 265 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: A 327 TYR cc_start: 0.8844 (t80) cc_final: 0.8617 (t80) REVERT: A 349 THR cc_start: 0.8623 (m) cc_final: 0.8236 (t) REVERT: A 352 LYS cc_start: 0.9186 (mtmm) cc_final: 0.8709 (mppt) REVERT: A 443 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7978 (ttp) REVERT: A 460 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8070 (tm-30) outliers start: 14 outliers final: 3 residues processed: 62 average time/residue: 1.1920 time to fit residues: 76.3800 Evaluate side-chains 46 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 443 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 21 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 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3614 Z= 0.264 Angle : 0.805 15.194 4896 Z= 0.398 Chirality : 0.046 0.179 566 Planarity : 0.004 0.041 622 Dihedral : 7.100 47.602 481 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.67 % Allowed : 14.44 % Favored : 84.89 % Rotamer: Outliers : 3.88 % Allowed : 14.47 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.46 % 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: -2.50 (0.37), residues: 450 helix: -0.07 (0.39), residues: 177 sheet: -1.61 (0.57), residues: 61 loop : -3.17 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 207 HIS 0.007 0.001 HIS A 51 PHE 0.010 0.001 PHE A 356 TYR 0.007 0.001 TYR A 113 ARG 0.006 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 39 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8536 (p90) cc_final: 0.7483 (p90) REVERT: A 198 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8269 (tttt) REVERT: A 265 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: A 460 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8075 (tm-30) outliers start: 15 outliers final: 3 residues processed: 51 average time/residue: 1.1135 time to fit residues: 58.8884 Evaluate side-chains 41 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 421 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 0.0570 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3614 Z= 0.197 Angle : 0.737 16.250 4896 Z= 0.367 Chirality : 0.046 0.234 566 Planarity : 0.004 0.038 622 Dihedral : 6.643 43.405 481 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.89 % Allowed : 12.22 % Favored : 86.89 % Rotamer: Outliers : 4.13 % Allowed : 16.28 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.46 % 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: -2.00 (0.39), residues: 450 helix: 0.50 (0.41), residues: 178 sheet: -1.36 (0.58), residues: 59 loop : -3.05 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 6 HIS 0.006 0.001 HIS A 51 PHE 0.019 0.001 PHE A 356 TYR 0.008 0.001 TYR A 327 ARG 0.004 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8497 (p90) cc_final: 0.7440 (p90) REVERT: A 198 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8258 (tttt) REVERT: A 302 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7103 (pp20) REVERT: A 460 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8107 (tm-30) outliers start: 16 outliers final: 6 residues processed: 57 average time/residue: 1.0838 time to fit residues: 64.0193 Evaluate side-chains 44 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 355 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 3614 Z= 0.461 Angle : 0.865 17.395 4896 Z= 0.422 Chirality : 0.049 0.227 566 Planarity : 0.006 0.088 622 Dihedral : 7.014 41.169 481 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.44 % Allowed : 15.33 % Favored : 84.22 % Rotamer: Outliers : 4.65 % Allowed : 17.57 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.46 % 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: -2.21 (0.38), residues: 450 helix: 0.25 (0.40), residues: 178 sheet: -1.68 (0.64), residues: 48 loop : -3.00 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 207 HIS 0.006 0.001 HIS A 191 PHE 0.022 0.003 PHE A 356 TYR 0.007 0.002 TYR A 256 ARG 0.003 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 39 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8258 (tttt) REVERT: A 358 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8363 (mm110) REVERT: A 460 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8110 (tm-30) outliers start: 18 outliers final: 8 residues processed: 52 average time/residue: 1.1660 time to fit residues: 62.9121 Evaluate side-chains 48 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 382 HIS Chi-restraints excluded: chain A residue 421 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.1980 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 38 GLN A 50 GLN A 154 GLN A 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3614 Z= 0.240 Angle : 0.770 16.586 4896 Z= 0.379 Chirality : 0.046 0.215 566 Planarity : 0.005 0.071 622 Dihedral : 6.731 40.702 481 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.33 % Favored : 86.44 % Rotamer: Outliers : 4.39 % Allowed : 18.86 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.46 % 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: -1.95 (0.39), residues: 450 helix: 0.46 (0.40), residues: 179 sheet: -1.58 (0.64), residues: 49 loop : -2.83 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 207 HIS 0.004 0.001 HIS A 191 PHE 0.024 0.002 PHE A 356 TYR 0.021 0.002 TYR A 108 ARG 0.003 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 41 time to evaluate : 0.430 Fit side-chains REVERT: A 92 TYR cc_start: 0.8539 (p90) cc_final: 0.7424 (p90) REVERT: A 198 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8246 (tttt) REVERT: A 302 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7354 (pp20) REVERT: A 352 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8492 (mtmt) REVERT: A 358 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8504 (mm110) outliers start: 17 outliers final: 6 residues processed: 56 average time/residue: 1.0541 time to fit residues: 61.3149 Evaluate side-chains 43 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 421 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3614 Z= 0.228 Angle : 0.793 18.505 4896 Z= 0.385 Chirality : 0.046 0.187 566 Planarity : 0.005 0.064 622 Dihedral : 6.548 40.959 481 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.22 % Favored : 85.56 % Rotamer: Outliers : 3.36 % Allowed : 20.16 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.46 % 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: -1.79 (0.39), residues: 450 helix: 0.64 (0.41), residues: 179 sheet: -1.40 (0.66), residues: 49 loop : -2.82 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 207 HIS 0.004 0.001 HIS A 191 PHE 0.007 0.001 PHE A 454 TYR 0.017 0.001 TYR A 108 ARG 0.002 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 92 TYR cc_start: 0.8532 (p90) cc_final: 0.7370 (p90) REVERT: A 198 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8242 (tttt) REVERT: A 302 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7336 (pp20) REVERT: A 358 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8570 (mm110) outliers start: 13 outliers final: 6 residues processed: 50 average time/residue: 1.1592 time to fit residues: 60.2024 Evaluate side-chains 44 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 421 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 3614 Z= 0.381 Angle : 0.843 18.981 4896 Z= 0.409 Chirality : 0.048 0.173 566 Planarity : 0.005 0.064 622 Dihedral : 6.780 39.766 481 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 15.56 % Favored : 84.22 % Rotamer: Outliers : 3.36 % Allowed : 20.67 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.69 % 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: -1.97 (0.39), residues: 450 helix: 0.44 (0.40), residues: 179 sheet: -1.50 (0.66), residues: 48 loop : -2.87 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 207 HIS 0.005 0.001 HIS A 191 PHE 0.015 0.002 PHE A 454 TYR 0.016 0.002 TYR A 108 ARG 0.003 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.468 Fit side-chains REVERT: A 92 TYR cc_start: 0.8571 (p90) cc_final: 0.7358 (p90) REVERT: A 198 LYS cc_start: 0.8559 (mmtt) cc_final: 0.8227 (tttt) REVERT: A 352 LYS cc_start: 0.9068 (mtmm) cc_final: 0.8475 (mtmt) REVERT: A 358 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8620 (mm110) outliers start: 13 outliers final: 9 residues processed: 52 average time/residue: 1.1021 time to fit residues: 59.5402 Evaluate side-chains 47 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 421 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 35 optimal weight: 0.0070 chunk 3 optimal weight: 0.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3614 Z= 0.205 Angle : 0.802 19.734 4896 Z= 0.386 Chirality : 0.046 0.151 566 Planarity : 0.004 0.057 622 Dihedral : 6.517 39.142 481 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.89 % Favored : 86.89 % Rotamer: Outliers : 2.58 % Allowed : 22.48 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.69 % 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: -1.61 (0.40), residues: 450 helix: 0.91 (0.42), residues: 173 sheet: -1.25 (0.68), residues: 49 loop : -2.75 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 6 HIS 0.003 0.001 HIS A 191 PHE 0.006 0.001 PHE A 146 TYR 0.015 0.001 TYR A 108 ARG 0.003 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.383 Fit side-chains REVERT: A 92 TYR cc_start: 0.8511 (p90) cc_final: 0.7371 (p90) REVERT: A 114 ASP cc_start: 0.8364 (t70) cc_final: 0.8119 (t0) REVERT: A 198 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8224 (tttt) REVERT: A 302 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7344 (pp20) REVERT: A 358 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8605 (mm110) outliers start: 10 outliers final: 5 residues processed: 49 average time/residue: 1.0758 time to fit residues: 54.7999 Evaluate side-chains 42 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 355 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.0170 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3614 Z= 0.247 Angle : 0.832 20.595 4896 Z= 0.395 Chirality : 0.047 0.163 566 Planarity : 0.004 0.055 622 Dihedral : 6.400 35.147 481 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 14.67 % Favored : 85.11 % Rotamer: Outliers : 2.58 % Allowed : 23.00 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.69 % 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: -1.62 (0.40), residues: 450 helix: 0.92 (0.42), residues: 173 sheet: -1.29 (0.68), residues: 49 loop : -2.77 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 207 HIS 0.004 0.001 HIS A 191 PHE 0.012 0.002 PHE A 356 TYR 0.015 0.001 TYR A 108 ARG 0.003 0.000 ARG A 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.442 Fit side-chains REVERT: A 92 TYR cc_start: 0.8536 (p90) cc_final: 0.7313 (p90) REVERT: A 114 ASP cc_start: 0.8384 (t70) cc_final: 0.8132 (t0) REVERT: A 198 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8235 (tttt) REVERT: A 302 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7348 (pp20) REVERT: A 358 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8621 (mm110) outliers start: 10 outliers final: 7 residues processed: 48 average time/residue: 1.0019 time to fit residues: 50.1381 Evaluate side-chains 45 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.130746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.102655 restraints weight = 6593.464| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.70 r_work: 0.3338 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3614 Z= 0.240 Angle : 0.844 20.327 4896 Z= 0.403 Chirality : 0.048 0.176 566 Planarity : 0.004 0.048 622 Dihedral : 6.295 34.637 481 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.56 % Favored : 86.22 % Rotamer: Outliers : 2.58 % Allowed : 23.00 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.69 % 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: -1.59 (0.40), residues: 450 helix: 0.93 (0.42), residues: 173 sheet: -1.22 (0.68), residues: 49 loop : -2.76 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 207 HIS 0.004 0.001 HIS A 191 PHE 0.013 0.001 PHE A 356 TYR 0.014 0.001 TYR A 108 ARG 0.003 0.000 ARG A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1789.08 seconds wall clock time: 32 minutes 32.66 seconds (1952.66 seconds total)