Starting phenix.real_space_refine on Thu Jul 18 19:37:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jts_36651/07_2024/8jts_36651.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jts_36651/07_2024/8jts_36651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jts_36651/07_2024/8jts_36651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jts_36651/07_2024/8jts_36651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jts_36651/07_2024/8jts_36651.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jts_36651/07_2024/8jts_36651.cif" } resolution = 4.14 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= 0.002 sd= 0.079 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 23 5.16 5 C 2190 2.51 5 N 534 2.21 5 O 583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 5": "OD1" <-> "OD2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A GLU 455": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3330 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3321 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 20, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 9, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 7, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 157 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.62, per 1000 atoms: 0.79 Number of scatterers: 3330 At special positions: 0 Unit cell: (94.1775, 58.455, 67.115, 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 23 16.00 O 583 8.00 N 534 7.00 C 2190 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: 1.38 Conformation dependent library (CDL) restraints added in 623.4 milliseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 850 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 77.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 32 through 37 removed outlier: 3.670A pdb=" N CYS A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 146 through 166 Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 174 through 195 Processing helix chain 'A' and resid 199 through 228 Processing helix chain 'A' and resid 232 through 258 Processing helix chain 'A' and resid 260 through 279 removed outlier: 3.668A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.896A pdb=" N TYR A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 340 through 368 Processing helix chain 'A' and resid 376 through 397 removed outlier: 3.657A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 403 through 423 removed outlier: 3.865A pdb=" N MET A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 456 removed outlier: 4.146A pdb=" N ILE A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 removed outlier: 4.081A pdb=" N ASN A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.855A pdb=" N CYS A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 491 Proline residue: A 481 - end of helix removed outlier: 3.888A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 510 removed outlier: 3.676A pdb=" N ILE A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.986A pdb=" N LEU A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 714 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: 0.82 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 533 1.30 - 1.43: 891 1.43 - 1.56: 1950 1.56 - 1.69: 0 1.69 - 1.82: 35 Bond restraints: 3409 Sorted by residual: bond pdb=" CA THR A 356 " pdb=" C THR A 356 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.27e-02 6.20e+03 7.52e+01 bond pdb=" C07 MF8 A 601 " pdb=" N08 MF8 A 601 " ideal model delta sigma weight residual 1.281 1.447 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" N ARG A 439 " pdb=" CA ARG A 439 " ideal model delta sigma weight residual 1.459 1.363 0.095 1.24e-02 6.50e+03 5.90e+01 bond pdb=" C07 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.393 1.245 0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" CA ASP A 357 " pdb=" CB ASP A 357 " ideal model delta sigma weight residual 1.530 1.432 0.098 1.57e-02 4.06e+03 3.91e+01 ... (remaining 3404 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.15: 76 105.15 - 112.36: 1743 112.36 - 119.57: 1130 119.57 - 126.78: 1665 126.78 - 133.99: 62 Bond angle restraints: 4676 Sorted by residual: angle pdb=" N THR A 356 " pdb=" CA THR A 356 " pdb=" C THR A 356 " ideal model delta sigma weight residual 111.07 102.52 8.55 1.07e+00 8.73e-01 6.38e+01 angle pdb=" C THR A 356 " pdb=" N ASP A 357 " pdb=" CA ASP A 357 " ideal model delta sigma weight residual 120.65 110.87 9.78 1.32e+00 5.74e-01 5.49e+01 angle pdb=" CA ASP A 357 " pdb=" C ASP A 357 " pdb=" N SER A 358 " ideal model delta sigma weight residual 116.92 124.94 -8.02 1.16e+00 7.43e-01 4.79e+01 angle pdb=" N GLN A 362 " pdb=" CA GLN A 362 " pdb=" C GLN A 362 " ideal model delta sigma weight residual 111.75 104.24 7.51 1.28e+00 6.10e-01 3.44e+01 angle pdb=" O ASP A 357 " pdb=" C ASP A 357 " pdb=" N SER A 358 " ideal model delta sigma weight residual 122.03 116.89 5.14 1.04e+00 9.25e-01 2.44e+01 ... (remaining 4671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 1767 17.47 - 34.94: 148 34.94 - 52.41: 29 52.41 - 69.89: 7 69.89 - 87.36: 3 Dihedral angle restraints: 1954 sinusoidal: 634 harmonic: 1320 Sorted by residual: dihedral pdb=" CA ILE A 442 " pdb=" C ILE A 442 " pdb=" N THR A 443 " pdb=" CA THR A 443 " ideal model delta harmonic sigma weight residual 180.00 151.77 28.23 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA THR A 356 " pdb=" C THR A 356 " pdb=" N ASP A 357 " pdb=" CA ASP A 357 " ideal model delta harmonic sigma weight residual 180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA MET A 448 " pdb=" C MET A 448 " pdb=" N ILE A 449 " pdb=" CA ILE A 449 " ideal model delta harmonic sigma weight residual 180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 1951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 465 0.056 - 0.112: 92 0.112 - 0.168: 8 0.168 - 0.224: 2 0.224 - 0.280: 4 Chirality restraints: 571 Sorted by residual: chirality pdb=" CG LEU A 25 " pdb=" CB LEU A 25 " pdb=" CD1 LEU A 25 " pdb=" CD2 LEU A 25 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ASP A 357 " pdb=" N ASP A 357 " pdb=" C ASP A 357 " pdb=" CB ASP A 357 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA TYR A 361 " pdb=" N TYR A 361 " pdb=" C TYR A 361 " pdb=" CB TYR A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 568 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 601 " -0.070 2.00e-02 2.50e+03 4.80e-01 5.19e+03 pdb=" C03 MF8 A 601 " 0.458 2.00e-02 2.50e+03 pdb=" C04 MF8 A 601 " -0.216 2.00e-02 2.50e+03 pdb=" C07 MF8 A 601 " 0.227 2.00e-02 2.50e+03 pdb=" N02 MF8 A 601 " 0.055 2.00e-02 2.50e+03 pdb=" N05 MF8 A 601 " -1.078 2.00e-02 2.50e+03 pdb=" N06 MF8 A 601 " 0.514 2.00e-02 2.50e+03 pdb=" N08 MF8 A 601 " -0.349 2.00e-02 2.50e+03 pdb=" N09 MF8 A 601 " 0.459 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.044 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO A 271 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 361 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C TYR A 361 " 0.041 2.00e-02 2.50e+03 pdb=" O TYR A 361 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN A 362 " -0.014 2.00e-02 2.50e+03 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 738 2.78 - 3.31: 3476 3.31 - 3.84: 5593 3.84 - 4.37: 5722 4.37 - 4.90: 9809 Nonbonded interactions: 25338 Sorted by model distance: nonbonded pdb=" O GLY A 167 " pdb=" ND2 ASN A 463 " model vdw 2.249 2.520 nonbonded pdb=" OG SER A 424 " pdb=" OD1 ASP A 426 " model vdw 2.315 2.440 nonbonded pdb=" O GLY A 12 " pdb=" NE2 GLN A 18 " model vdw 2.327 2.520 nonbonded pdb=" OD1 ASN A 198 " pdb=" OG SER A 201 " model vdw 2.345 2.440 nonbonded pdb=" O VAL A 141 " pdb=" OG SER A 145 " model vdw 2.367 2.440 ... (remaining 25333 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.020 Find NCS groups from input model: 0.030 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.166 3409 Z= 0.445 Angle : 0.933 9.780 4676 Z= 0.539 Chirality : 0.049 0.280 571 Planarity : 0.021 0.480 582 Dihedral : 14.111 87.356 1104 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.31 % Allowed : 0.94 % Favored : 98.75 % 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: -0.32 (0.39), residues: 457 helix: 0.25 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.17 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 354 HIS 0.001 0.000 HIS A 260 PHE 0.021 0.002 PHE A 151 TYR 0.010 0.001 TYR A 256 ARG 0.006 0.001 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.344 Fit side-chains REVERT: A 137 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6584 (mm-30) REVERT: A 293 LYS cc_start: 0.8310 (mttm) cc_final: 0.8109 (mttm) REVERT: A 352 TYR cc_start: 0.5406 (m-80) cc_final: 0.5079 (m-80) REVERT: A 361 TYR cc_start: 0.8688 (t80) cc_final: 0.8330 (t80) REVERT: A 449 ILE cc_start: 0.8890 (tt) cc_final: 0.8569 (tt) outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.1128 time to fit residues: 13.6154 Evaluate side-chains 80 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.0030 chunk 41 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3409 Z= 0.177 Angle : 0.590 6.842 4676 Z= 0.295 Chirality : 0.039 0.161 571 Planarity : 0.005 0.062 582 Dihedral : 4.423 19.951 479 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % 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: 0.33 (0.40), residues: 457 helix: 0.80 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.20 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 217 HIS 0.002 0.000 HIS A 260 PHE 0.021 0.001 PHE A 41 TYR 0.011 0.001 TYR A 256 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.272 Fit side-chains REVERT: A 137 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6596 (mm-30) REVERT: A 352 TYR cc_start: 0.5342 (m-80) cc_final: 0.5120 (m-80) REVERT: A 361 TYR cc_start: 0.8453 (t80) cc_final: 0.7992 (t80) REVERT: A 449 ILE cc_start: 0.8895 (tt) cc_final: 0.8547 (tt) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1146 time to fit residues: 14.2632 Evaluate side-chains 82 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3409 Z= 0.184 Angle : 0.608 7.372 4676 Z= 0.299 Chirality : 0.040 0.168 571 Planarity : 0.005 0.061 582 Dihedral : 4.270 18.450 479 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.40), residues: 457 helix: 1.26 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -0.96 (0.58), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.001 0.000 HIS A 260 PHE 0.016 0.001 PHE A 41 TYR 0.014 0.001 TYR A 361 ARG 0.003 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.360 Fit side-chains REVERT: A 137 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6609 (mm-30) REVERT: A 449 ILE cc_start: 0.8827 (tt) cc_final: 0.8589 (tt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1122 time to fit residues: 13.8883 Evaluate side-chains 81 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3409 Z= 0.181 Angle : 0.607 7.267 4676 Z= 0.298 Chirality : 0.040 0.204 571 Planarity : 0.005 0.061 582 Dihedral : 4.193 17.276 479 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.31 % Allowed : 4.69 % Favored : 95.00 % 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 (0.41), residues: 457 helix: 1.35 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.07 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 PHE 0.022 0.002 PHE A 151 TYR 0.011 0.001 TYR A 361 ARG 0.003 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.360 Fit side-chains REVERT: A 137 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6692 (mm-30) REVERT: A 287 ARG cc_start: 0.8645 (ttm-80) cc_final: 0.8351 (ttm-80) REVERT: A 352 TYR cc_start: 0.5379 (m-80) cc_final: 0.5099 (m-80) REVERT: A 449 ILE cc_start: 0.8840 (tt) cc_final: 0.8606 (tt) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1075 time to fit residues: 13.1699 Evaluate side-chains 82 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 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 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3409 Z= 0.193 Angle : 0.614 6.736 4676 Z= 0.307 Chirality : 0.040 0.175 571 Planarity : 0.005 0.060 582 Dihedral : 4.249 16.412 479 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % 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 (0.41), residues: 457 helix: 1.30 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.08 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 PHE 0.021 0.002 PHE A 41 TYR 0.012 0.001 TYR A 256 ARG 0.003 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.371 Fit side-chains REVERT: A 137 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6465 (mm-30) REVERT: A 449 ILE cc_start: 0.8867 (tt) cc_final: 0.8652 (tt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1079 time to fit residues: 13.3668 Evaluate side-chains 84 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 0.0060 chunk 36 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.0170 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.4634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3409 Z= 0.172 Angle : 0.606 6.909 4676 Z= 0.296 Chirality : 0.039 0.163 571 Planarity : 0.005 0.059 582 Dihedral : 4.170 15.236 479 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.41), residues: 457 helix: 1.39 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.09 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 PHE 0.016 0.001 PHE A 41 TYR 0.009 0.001 TYR A 256 ARG 0.003 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.383 Fit side-chains REVERT: A 137 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6378 (mm-30) REVERT: A 287 ARG cc_start: 0.8684 (ttm-80) cc_final: 0.8387 (ttm-80) REVERT: A 352 TYR cc_start: 0.5286 (m-80) cc_final: 0.4955 (m-80) REVERT: A 449 ILE cc_start: 0.8845 (tt) cc_final: 0.8594 (tt) REVERT: A 468 VAL cc_start: 0.7576 (p) cc_final: 0.7290 (p) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1106 time to fit residues: 13.5491 Evaluate side-chains 86 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 50.0000 chunk 44 optimal weight: 0.0170 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3409 Z= 0.192 Angle : 0.620 6.566 4676 Z= 0.309 Chirality : 0.041 0.248 571 Planarity : 0.005 0.059 582 Dihedral : 4.238 15.813 479 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.41), residues: 457 helix: 1.44 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -1.06 (0.59), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 PHE 0.030 0.002 PHE A 151 TYR 0.012 0.001 TYR A 256 ARG 0.003 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.348 Fit side-chains REVERT: A 137 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6295 (mm-30) REVERT: A 287 ARG cc_start: 0.8729 (ttm-80) cc_final: 0.8414 (ttm-80) REVERT: A 449 ILE cc_start: 0.8891 (tt) cc_final: 0.8632 (tt) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1101 time to fit residues: 13.9315 Evaluate side-chains 88 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3409 Z= 0.175 Angle : 0.626 8.008 4676 Z= 0.308 Chirality : 0.039 0.199 571 Planarity : 0.004 0.059 582 Dihedral : 4.144 15.690 479 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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 (0.41), residues: 457 helix: 1.53 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.10 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 288 HIS 0.001 0.000 HIS A 260 PHE 0.019 0.001 PHE A 41 TYR 0.010 0.001 TYR A 256 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.332 Fit side-chains REVERT: A 287 ARG cc_start: 0.8730 (ttm-80) cc_final: 0.8385 (ttm-80) REVERT: A 468 VAL cc_start: 0.7675 (p) cc_final: 0.7357 (p) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1151 time to fit residues: 13.9749 Evaluate side-chains 86 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3409 Z= 0.198 Angle : 0.647 7.872 4676 Z= 0.322 Chirality : 0.041 0.235 571 Planarity : 0.005 0.059 582 Dihedral : 4.231 17.196 479 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 1.10 (0.41), residues: 457 helix: 1.45 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -1.04 (0.59), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 PHE 0.031 0.002 PHE A 151 TYR 0.012 0.001 TYR A 256 ARG 0.004 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.382 Fit side-chains REVERT: A 137 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6685 (mm-30) REVERT: A 352 TYR cc_start: 0.5502 (m-80) cc_final: 0.5162 (m-80) REVERT: A 449 ILE cc_start: 0.8957 (tt) cc_final: 0.8734 (tt) REVERT: A 468 VAL cc_start: 0.7726 (p) cc_final: 0.7462 (p) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1077 time to fit residues: 13.6472 Evaluate side-chains 86 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 10 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 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3409 Z= 0.189 Angle : 0.648 7.898 4676 Z= 0.318 Chirality : 0.041 0.225 571 Planarity : 0.005 0.058 582 Dihedral : 4.199 17.576 479 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.10 (0.41), residues: 457 helix: 1.42 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.01 (0.60), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 PHE 0.019 0.002 PHE A 41 TYR 0.010 0.001 TYR A 256 ARG 0.004 0.000 ARG A 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.360 Fit side-chains REVERT: A 449 ILE cc_start: 0.8954 (tt) cc_final: 0.8701 (tt) REVERT: A 468 VAL cc_start: 0.7699 (p) cc_final: 0.7461 (p) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1062 time to fit residues: 13.3589 Evaluate side-chains 86 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.0570 chunk 32 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 0.0040 chunk 41 optimal weight: 0.3980 chunk 24 optimal weight: 30.0000 chunk 31 optimal weight: 0.7980 overall best weight: 0.2710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.218598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.192286 restraints weight = 4675.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.197312 restraints weight = 2545.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.200437 restraints weight = 1621.162| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3409 Z= 0.162 Angle : 0.631 8.363 4676 Z= 0.303 Chirality : 0.039 0.190 571 Planarity : 0.005 0.058 582 Dihedral : 4.060 16.904 479 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.41), residues: 457 helix: 1.56 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.01 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 146 HIS 0.001 0.000 HIS A 260 PHE 0.029 0.001 PHE A 151 TYR 0.007 0.001 TYR A 256 ARG 0.003 0.000 ARG A 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1014.30 seconds wall clock time: 18 minutes 57.49 seconds (1137.49 seconds total)