Starting phenix.real_space_refine on Mon Jun 24 14:21:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/06_2024/8zms_60255_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/06_2024/8zms_60255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/06_2024/8zms_60255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/06_2024/8zms_60255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/06_2024/8zms_60255_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zms_60255/06_2024/8zms_60255_updated.pdb" } resolution = 3.7 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= 0.020 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 17 5.16 5 C 1940 2.51 5 N 463 2.21 5 O 500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 284": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 2920 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2910 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 24, 'TRANS': 361} Chain breaks: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.72, per 1000 atoms: 0.93 Number of scatterers: 2920 At special positions: 0 Unit cell: (70.55, 59.76, 83.83, 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 17 16.00 O 500 8.00 N 463 7.00 C 1940 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 - 3.50 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: 1.05 Conformation dependent library (CDL) restraints added in 680.2 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 716 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 0 sheets defined 80.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 22 through 60 removed outlier: 3.608A pdb=" N VAL A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Proline residue: A 55 - end of helix Proline residue: A 58 - end of helix Processing helix chain 'A' and resid 123 through 148 removed outlier: 3.577A pdb=" N ASN A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 152 through 170 Processing helix chain 'A' and resid 175 through 200 removed outlier: 4.660A pdb=" N THR A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 237 Proline residue: A 229 - end of helix removed outlier: 4.174A pdb=" N LEU A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 263 removed outlier: 3.926A pdb=" N LEU A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.606A pdb=" N LYS A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 356 through 372 Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 380 through 412 Proline residue: A 403 - end of helix Processing helix chain 'A' and resid 419 through 445 removed outlier: 4.151A pdb=" N ALA A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Proline residue: A 436 - end of helix removed outlier: 4.386A pdb=" N GLY A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 468 Proline residue: A 464 - end of helix removed outlier: 4.776A pdb=" N LEU A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU A 468 " --> pdb=" O PRO A 464 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 627 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: 0.78 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 450 1.31 - 1.43: 765 1.43 - 1.56: 1746 1.56 - 1.68: 0 1.68 - 1.81: 28 Bond restraints: 2989 Sorted by residual: bond pdb=" C5 ACH A1001 " pdb=" O4 ACH A1001 " ideal model delta sigma weight residual 1.335 1.410 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C2 ACH A1001 " pdb=" C3 ACH A1001 " ideal model delta sigma weight residual 1.509 1.553 -0.044 2.00e-02 2.50e+03 4.86e+00 bond pdb=" C5 ACH A1001 " pdb=" C6 ACH A1001 " ideal model delta sigma weight residual 1.497 1.541 -0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" CA VAL A 336 " pdb=" C VAL A 336 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 3.04e+00 bond pdb=" C ILE A 303 " pdb=" N PRO A 304 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 2.99e+00 ... (remaining 2984 not shown) Histogram of bond angle deviations from ideal: 99.98 - 107.00: 127 107.00 - 114.02: 1714 114.02 - 121.04: 1556 121.04 - 128.06: 651 128.06 - 135.09: 34 Bond angle restraints: 4082 Sorted by residual: angle pdb=" C PHE A 335 " pdb=" N VAL A 336 " pdb=" CA VAL A 336 " ideal model delta sigma weight residual 120.24 123.54 -3.30 6.30e-01 2.52e+00 2.74e+01 angle pdb=" N PRO A 229 " pdb=" CA PRO A 229 " pdb=" C PRO A 229 " ideal model delta sigma weight residual 110.70 115.83 -5.13 1.22e+00 6.72e-01 1.77e+01 angle pdb=" CA PRO A 229 " pdb=" C PRO A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 117.93 122.77 -4.84 1.20e+00 6.94e-01 1.63e+01 angle pdb=" N VAL A 374 " pdb=" CA VAL A 374 " pdb=" C VAL A 374 " ideal model delta sigma weight residual 108.88 116.63 -7.75 2.16e+00 2.14e-01 1.29e+01 angle pdb=" C10 ACH A1001 " pdb=" N1 ACH A1001 " pdb=" C9 ACH A1001 " ideal model delta sigma weight residual 108.54 119.26 -10.72 3.00e+00 1.11e-01 1.28e+01 ... (remaining 4077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.28: 1595 11.28 - 22.57: 128 22.57 - 33.85: 26 33.85 - 45.13: 10 45.13 - 56.42: 3 Dihedral angle restraints: 1762 sinusoidal: 648 harmonic: 1114 Sorted by residual: dihedral pdb=" CA SER A 379 " pdb=" C SER A 379 " pdb=" N PHE A 380 " pdb=" CA PHE A 380 " ideal model delta harmonic sigma weight residual -180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ASP A 288 " pdb=" C ASP A 288 " pdb=" N PRO A 289 " pdb=" CA PRO A 289 " ideal model delta harmonic sigma weight residual -180.00 -162.35 -17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA GLU A 206 " pdb=" C GLU A 206 " pdb=" N GLU A 207 " pdb=" CA GLU A 207 " ideal model delta harmonic sigma weight residual -180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 1759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 341 0.049 - 0.098: 113 0.098 - 0.147: 36 0.147 - 0.195: 6 0.195 - 0.244: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" CB VAL A 54 " pdb=" CA VAL A 54 " pdb=" CG1 VAL A 54 " pdb=" CG2 VAL A 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CG LEU A 178 " pdb=" CB LEU A 178 " pdb=" CD1 LEU A 178 " pdb=" CD2 LEU A 178 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA ASN A 139 " pdb=" N ASN A 139 " pdb=" C ASN A 139 " pdb=" CB ASN A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 494 not shown) Planarity restraints: 501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 309 " 0.044 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO A 310 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 224 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.69e+00 pdb=" C GLY A 224 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY A 224 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 225 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 228 " 0.037 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 229 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " 0.031 5.00e-02 4.00e+02 ... (remaining 498 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 933 2.86 - 3.37: 2910 3.37 - 3.88: 4884 3.88 - 4.39: 5123 4.39 - 4.90: 8763 Nonbonded interactions: 22613 Sorted by model distance: nonbonded pdb=" O LEU A 127 " pdb=" OG SER A 130 " model vdw 2.349 2.440 nonbonded pdb=" O ASP A 174 " pdb=" OG1 THR A 177 " model vdw 2.358 2.440 nonbonded pdb=" OD2 ASP A 147 " pdb=" OG SER A 419 " model vdw 2.359 2.440 nonbonded pdb=" ND2 ASN A 139 " pdb=" OD2 ASP A 425 " model vdw 2.390 2.520 nonbonded pdb=" O GLN A 135 " pdb=" ND2 ASN A 139 " model vdw 2.412 2.520 ... (remaining 22608 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 group one per residue 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: 1.540 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: 6.690 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.660 Find NCS groups from input model: 0.080 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 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 0.075 2989 Z= 0.422 Angle : 1.147 10.721 4082 Z= 0.589 Chirality : 0.055 0.244 497 Planarity : 0.010 0.066 501 Dihedral : 9.676 56.418 1046 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % 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: -3.71 (0.32), residues: 380 helix: -2.04 (0.21), residues: 301 sheet: None (None), residues: 0 loop : -3.30 (0.64), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 325 HIS 0.005 0.001 HIS A 338 PHE 0.019 0.003 PHE A 238 TYR 0.014 0.002 TYR A 50 ARG 0.002 0.001 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.290 Fit side-chains REVERT: A 21 GLU cc_start: 0.7771 (tt0) cc_final: 0.7280 (pm20) REVERT: A 254 PHE cc_start: 0.7232 (t80) cc_final: 0.7026 (m-80) REVERT: A 286 MET cc_start: 0.5604 (mmp) cc_final: 0.4183 (ttm) REVERT: A 305 LEU cc_start: 0.8372 (mt) cc_final: 0.8097 (mt) REVERT: A 429 SER cc_start: 0.8595 (m) cc_final: 0.8097 (p) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1307 time to fit residues: 14.3278 Evaluate side-chains 65 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 19 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2989 Z= 0.222 Angle : 0.704 7.161 4082 Z= 0.341 Chirality : 0.041 0.114 497 Planarity : 0.006 0.046 501 Dihedral : 5.795 47.032 415 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.61 % Allowed : 11.76 % Favored : 85.62 % 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: -1.04 (0.41), residues: 380 helix: -0.12 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -2.96 (0.70), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 325 HIS 0.002 0.000 HIS A 283 PHE 0.026 0.002 PHE A 169 TYR 0.011 0.002 TYR A 428 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.314 Fit side-chains REVERT: A 21 GLU cc_start: 0.7907 (tt0) cc_final: 0.7200 (pm20) REVERT: A 286 MET cc_start: 0.5653 (mmp) cc_final: 0.4196 (ttp) REVERT: A 324 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6603 (mt-10) outliers start: 8 outliers final: 6 residues processed: 75 average time/residue: 0.0905 time to fit residues: 9.0638 Evaluate side-chains 70 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 427 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2989 Z= 0.242 Angle : 0.713 7.773 4082 Z= 0.345 Chirality : 0.041 0.125 497 Planarity : 0.005 0.040 501 Dihedral : 5.505 42.305 415 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.25 % Allowed : 14.71 % Favored : 81.05 % 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: -0.10 (0.44), residues: 380 helix: 0.57 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -2.92 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 325 HIS 0.002 0.001 HIS A 444 PHE 0.022 0.002 PHE A 169 TYR 0.010 0.002 TYR A 432 ARG 0.002 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.314 Fit side-chains REVERT: A 21 GLU cc_start: 0.7960 (tt0) cc_final: 0.7125 (pm20) REVERT: A 286 MET cc_start: 0.5778 (mmp) cc_final: 0.4310 (ttp) REVERT: A 299 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8309 (m) REVERT: A 410 ASP cc_start: 0.8126 (m-30) cc_final: 0.7810 (m-30) outliers start: 13 outliers final: 10 residues processed: 66 average time/residue: 0.0975 time to fit residues: 8.5335 Evaluate side-chains 68 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 427 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2989 Z= 0.242 Angle : 0.691 7.628 4082 Z= 0.334 Chirality : 0.041 0.117 497 Planarity : 0.005 0.040 501 Dihedral : 5.420 43.245 415 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.90 % Allowed : 15.36 % Favored : 79.74 % 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: 0.36 (0.45), residues: 380 helix: 0.91 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -2.82 (0.75), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 357 HIS 0.002 0.001 HIS A 283 PHE 0.020 0.002 PHE A 169 TYR 0.011 0.002 TYR A 432 ARG 0.002 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 0.305 Fit side-chains REVERT: A 286 MET cc_start: 0.5932 (mmp) cc_final: 0.4280 (ttp) REVERT: A 410 ASP cc_start: 0.8148 (m-30) cc_final: 0.7862 (m-30) outliers start: 15 outliers final: 9 residues processed: 64 average time/residue: 0.0838 time to fit residues: 7.5005 Evaluate side-chains 64 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 427 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.0470 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.0570 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.0870 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2989 Z= 0.184 Angle : 0.661 8.212 4082 Z= 0.314 Chirality : 0.039 0.117 497 Planarity : 0.005 0.042 501 Dihedral : 5.132 41.586 415 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.90 % Allowed : 16.01 % Favored : 79.08 % 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: 0.69 (0.46), residues: 380 helix: 1.13 (0.31), residues: 314 sheet: None (None), residues: 0 loop : -2.76 (0.78), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 357 HIS 0.002 0.000 HIS A 283 PHE 0.017 0.001 PHE A 169 TYR 0.009 0.001 TYR A 359 ARG 0.001 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 0.327 Fit side-chains REVERT: A 51 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7379 (mmm) REVERT: A 286 MET cc_start: 0.5889 (mmp) cc_final: 0.4254 (ttp) REVERT: A 410 ASP cc_start: 0.8130 (m-30) cc_final: 0.7846 (m-30) outliers start: 15 outliers final: 8 residues processed: 64 average time/residue: 0.1049 time to fit residues: 8.9250 Evaluate side-chains 61 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 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 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2989 Z= 0.233 Angle : 0.696 7.210 4082 Z= 0.330 Chirality : 0.041 0.120 497 Planarity : 0.005 0.042 501 Dihedral : 5.180 41.845 415 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.58 % Allowed : 16.99 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.45), residues: 380 helix: 1.32 (0.30), residues: 305 sheet: None (None), residues: 0 loop : -2.66 (0.76), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 357 HIS 0.002 0.001 HIS A 283 PHE 0.010 0.001 PHE A 169 TYR 0.010 0.001 TYR A 432 ARG 0.002 0.000 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.329 Fit side-chains REVERT: A 286 MET cc_start: 0.6057 (mmp) cc_final: 0.4306 (ttp) REVERT: A 410 ASP cc_start: 0.8222 (m-30) cc_final: 0.7938 (m-30) outliers start: 14 outliers final: 11 residues processed: 60 average time/residue: 0.0858 time to fit residues: 7.1181 Evaluate side-chains 62 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 0.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2989 Z= 0.222 Angle : 0.685 7.117 4082 Z= 0.325 Chirality : 0.040 0.118 497 Planarity : 0.005 0.041 501 Dihedral : 5.161 41.621 415 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.25 % Allowed : 16.67 % Favored : 79.08 % 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: 0.94 (0.45), residues: 380 helix: 1.39 (0.30), residues: 304 sheet: None (None), residues: 0 loop : -2.56 (0.76), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 357 HIS 0.002 0.001 HIS A 283 PHE 0.012 0.001 PHE A 169 TYR 0.010 0.001 TYR A 432 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.313 Fit side-chains REVERT: A 51 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7493 (mmm) REVERT: A 286 MET cc_start: 0.6165 (mmp) cc_final: 0.4370 (ttp) REVERT: A 410 ASP cc_start: 0.8156 (m-30) cc_final: 0.7834 (m-30) outliers start: 13 outliers final: 9 residues processed: 62 average time/residue: 0.0806 time to fit residues: 6.9321 Evaluate side-chains 63 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.0870 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2989 Z= 0.218 Angle : 0.684 7.085 4082 Z= 0.325 Chirality : 0.040 0.117 497 Planarity : 0.005 0.042 501 Dihedral : 5.271 46.416 415 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.25 % Allowed : 16.67 % Favored : 79.08 % 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: 0.94 (0.45), residues: 380 helix: 1.40 (0.30), residues: 303 sheet: None (None), residues: 0 loop : -2.54 (0.76), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 357 HIS 0.002 0.001 HIS A 283 PHE 0.014 0.001 PHE A 169 TYR 0.009 0.001 TYR A 359 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.285 Fit side-chains REVERT: A 51 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7355 (mmm) REVERT: A 286 MET cc_start: 0.6165 (mmp) cc_final: 0.4400 (ttp) REVERT: A 299 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8200 (m) REVERT: A 410 ASP cc_start: 0.8158 (m-30) cc_final: 0.7837 (m-30) outliers start: 13 outliers final: 9 residues processed: 63 average time/residue: 0.0802 time to fit residues: 7.0621 Evaluate side-chains 64 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2989 Z= 0.215 Angle : 0.683 6.992 4082 Z= 0.323 Chirality : 0.040 0.118 497 Planarity : 0.005 0.042 501 Dihedral : 5.206 43.647 415 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.92 % Allowed : 16.99 % Favored : 79.08 % 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: 0.98 (0.45), residues: 380 helix: 1.50 (0.31), residues: 296 sheet: None (None), residues: 0 loop : -2.51 (0.71), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 357 HIS 0.002 0.001 HIS A 283 PHE 0.013 0.001 PHE A 169 TYR 0.009 0.001 TYR A 359 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.303 Fit side-chains REVERT: A 51 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7362 (mmm) REVERT: A 286 MET cc_start: 0.6108 (mmp) cc_final: 0.4374 (ttp) REVERT: A 299 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8207 (m) REVERT: A 332 LEU cc_start: 0.8442 (tt) cc_final: 0.8143 (tp) REVERT: A 410 ASP cc_start: 0.8135 (m-30) cc_final: 0.7830 (m-30) outliers start: 12 outliers final: 8 residues processed: 62 average time/residue: 0.0793 time to fit residues: 6.8561 Evaluate side-chains 61 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.0470 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.0470 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2989 Z= 0.194 Angle : 0.669 6.876 4082 Z= 0.315 Chirality : 0.040 0.114 497 Planarity : 0.005 0.042 501 Dihedral : 5.137 44.060 415 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.94 % Allowed : 16.99 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.46), residues: 380 helix: 1.82 (0.31), residues: 290 sheet: None (None), residues: 0 loop : -2.40 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 357 HIS 0.001 0.000 HIS A 283 PHE 0.013 0.001 PHE A 169 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG A 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.328 Fit side-chains REVERT: A 51 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7182 (mmm) REVERT: A 286 MET cc_start: 0.6199 (mmp) cc_final: 0.4417 (ttp) REVERT: A 299 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8232 (m) REVERT: A 332 LEU cc_start: 0.8447 (tt) cc_final: 0.8118 (tp) REVERT: A 410 ASP cc_start: 0.8114 (m-30) cc_final: 0.7805 (m-30) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.0816 time to fit residues: 6.7949 Evaluate side-chains 59 residues out of total 306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 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 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.177442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.162641 restraints weight = 4672.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.166421 restraints weight = 2495.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.168889 restraints weight = 1540.043| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2989 Z= 0.221 Angle : 0.701 8.569 4082 Z= 0.331 Chirality : 0.041 0.131 497 Planarity : 0.005 0.042 501 Dihedral : 5.191 43.177 415 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.61 % Allowed : 17.97 % Favored : 79.41 % 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: 1.18 (0.46), residues: 380 helix: 1.67 (0.31), residues: 295 sheet: None (None), residues: 0 loop : -2.51 (0.70), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 357 HIS 0.002 0.001 HIS A 283 PHE 0.012 0.001 PHE A 169 TYR 0.011 0.001 TYR A 50 ARG 0.002 0.000 ARG A 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1054.68 seconds wall clock time: 19 minutes 31.12 seconds (1171.12 seconds total)