Starting phenix.real_space_refine on Sun Mar 10 16:46:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6a_17462/03_2024/8p6a_17462.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6a_17462/03_2024/8p6a_17462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6a_17462/03_2024/8p6a_17462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6a_17462/03_2024/8p6a_17462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6a_17462/03_2024/8p6a_17462.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6a_17462/03_2024/8p6a_17462.pdb" } resolution = 3.63 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= 0.048 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 16 5.16 5 C 2225 2.51 5 N 531 2.21 5 O 565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 44": "OE1" <-> "OE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 314": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3337 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3337 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 15, 'TRANS': 416} Chain breaks: 3 Time building chain proxies: 2.37, per 1000 atoms: 0.71 Number of scatterers: 3337 At special positions: 0 Unit cell: (72.384, 67.392, 65.728, 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 16 16.00 O 565 8.00 N 531 7.00 C 2225 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: 1.22 Conformation dependent library (CDL) restraints added in 633.5 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 790 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 1 sheets defined 80.6% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 35 through 62 removed outlier: 5.178A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 96 removed outlier: 3.984A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 157 through 182 removed outlier: 4.188A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 183 through 186 Processing helix chain 'A' and resid 187 through 220 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.685A pdb=" N THR A 224 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 244 Processing helix chain 'A' and resid 311 through 346 removed outlier: 3.690A pdb=" N VAL A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 367 through 370 removed outlier: 3.915A pdb=" N THR A 370 " --> pdb=" O ALA A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 370' Processing helix chain 'A' and resid 371 through 396 Proline residue: A 382 - end of helix Proline residue: A 390 - end of helix Processing helix chain 'A' and resid 400 through 433 removed outlier: 3.632A pdb=" N ARG A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 Processing helix chain 'A' and resid 454 through 479 removed outlier: 4.047A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 511 Processing helix chain 'A' and resid 532 through 559 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 258 hydrogen bonds defined for protein. 762 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: 0.91 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1002 1.34 - 1.46: 751 1.46 - 1.58: 1641 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3420 Sorted by residual: bond pdb=" CA VAL A 322 " pdb=" C VAL A 322 " ideal model delta sigma weight residual 1.520 1.532 -0.013 8.80e-03 1.29e+04 2.04e+00 bond pdb=" CB ASP A 185 " pdb=" CG ASP A 185 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.21e+00 bond pdb=" CB ASP A 97 " pdb=" CG ASP A 97 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.20e+00 bond pdb=" C ALA A 65 " pdb=" N PRO A 66 " ideal model delta sigma weight residual 1.340 1.367 -0.027 2.76e-02 1.31e+03 9.38e-01 bond pdb=" CG LEU A 46 " pdb=" CD2 LEU A 46 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.25e-01 ... (remaining 3415 not shown) Histogram of bond angle deviations from ideal: 96.77 - 104.21: 40 104.21 - 111.65: 1617 111.65 - 119.10: 1122 119.10 - 126.54: 1814 126.54 - 133.98: 55 Bond angle restraints: 4648 Sorted by residual: angle pdb=" CB MET A 117 " pdb=" CG MET A 117 " pdb=" SD MET A 117 " ideal model delta sigma weight residual 112.70 124.25 -11.55 3.00e+00 1.11e-01 1.48e+01 angle pdb=" CA LEU A 344 " pdb=" CB LEU A 344 " pdb=" CG LEU A 344 " ideal model delta sigma weight residual 116.30 125.21 -8.91 3.50e+00 8.16e-02 6.48e+00 angle pdb=" CA LEU A 79 " pdb=" CB LEU A 79 " pdb=" CG LEU A 79 " ideal model delta sigma weight residual 116.30 124.51 -8.21 3.50e+00 8.16e-02 5.50e+00 angle pdb=" CA LEU A 507 " pdb=" CB LEU A 507 " pdb=" CG LEU A 507 " ideal model delta sigma weight residual 116.30 123.81 -7.51 3.50e+00 8.16e-02 4.61e+00 angle pdb=" CA LEU A 42 " pdb=" CB LEU A 42 " pdb=" CG LEU A 42 " ideal model delta sigma weight residual 116.30 123.70 -7.40 3.50e+00 8.16e-02 4.47e+00 ... (remaining 4643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 1602 15.10 - 30.19: 252 30.19 - 45.29: 75 45.29 - 60.38: 30 60.38 - 75.48: 4 Dihedral angle restraints: 1963 sinusoidal: 729 harmonic: 1234 Sorted by residual: dihedral pdb=" CG ARG A 193 " pdb=" CD ARG A 193 " pdb=" NE ARG A 193 " pdb=" CZ ARG A 193 " ideal model delta sinusoidal sigma weight residual 180.00 135.59 44.41 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG A 404 " pdb=" CD ARG A 404 " pdb=" NE ARG A 404 " pdb=" CZ ARG A 404 " ideal model delta sinusoidal sigma weight residual -180.00 -137.22 -42.78 2 1.50e+01 4.44e-03 9.84e+00 dihedral pdb=" CB ARG A 404 " pdb=" CG ARG A 404 " pdb=" CD ARG A 404 " pdb=" NE ARG A 404 " ideal model delta sinusoidal sigma weight residual 180.00 122.86 57.14 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 1960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 401 0.043 - 0.086: 118 0.086 - 0.129: 20 0.129 - 0.173: 4 0.173 - 0.216: 1 Chirality restraints: 544 Sorted by residual: chirality pdb=" CB ILE A 329 " pdb=" CA ILE A 329 " pdb=" CG1 ILE A 329 " pdb=" CG2 ILE A 329 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB VAL A 246 " pdb=" CA VAL A 246 " pdb=" CG1 VAL A 246 " pdb=" CG2 VAL A 246 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA VAL A 455 " pdb=" N VAL A 455 " pdb=" C VAL A 455 " pdb=" CB VAL A 455 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 541 not shown) Planarity restraints: 567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 457 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" CD GLN A 457 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLN A 457 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN A 457 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 455 " -0.023 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO A 456 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 385 " -0.005 2.00e-02 2.50e+03 1.10e-02 1.20e+00 pdb=" C ASP A 385 " 0.019 2.00e-02 2.50e+03 pdb=" O ASP A 385 " -0.007 2.00e-02 2.50e+03 pdb=" N LYS A 386 " -0.006 2.00e-02 2.50e+03 ... (remaining 564 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 82 2.71 - 3.26: 3478 3.26 - 3.80: 5677 3.80 - 4.35: 6172 4.35 - 4.90: 10711 Nonbonded interactions: 26120 Sorted by model distance: nonbonded pdb=" OG SER A 415 " pdb=" OE1 GLN A 457 " model vdw 2.161 2.440 nonbonded pdb=" O SER A 415 " pdb=" NE2 GLN A 457 " model vdw 2.239 2.520 nonbonded pdb=" OH TYR A 342 " pdb=" OE1 GLN A 457 " model vdw 2.302 2.440 nonbonded pdb=" O ARG A 394 " pdb=" NH1 ARG A 394 " model vdw 2.372 2.520 nonbonded pdb=" OG SER A 109 " pdb=" O GLY A 167 " model vdw 2.394 2.440 ... (remaining 26115 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.120 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.110 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 : 0.003 0.032 3420 Z= 0.201 Angle : 0.656 11.546 4648 Z= 0.313 Chirality : 0.041 0.216 544 Planarity : 0.003 0.034 567 Dihedral : 17.396 75.475 1173 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.29 % Allowed : 39.48 % Favored : 60.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.43), residues: 424 helix: 2.59 (0.29), residues: 325 sheet: -1.95 (1.74), residues: 10 loop : -0.54 (0.73), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 368 HIS 0.002 0.000 HIS A 348 PHE 0.013 0.001 PHE A 247 TYR 0.013 0.001 TYR A 444 ARG 0.001 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.380 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.1434 time to fit residues: 13.1931 Evaluate side-chains 73 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN A 528 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3420 Z= 0.183 Angle : 0.553 7.100 4648 Z= 0.272 Chirality : 0.038 0.145 544 Planarity : 0.003 0.030 567 Dihedral : 3.869 29.642 459 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.75 % Allowed : 35.73 % Favored : 60.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.43), residues: 424 helix: 2.74 (0.29), residues: 325 sheet: -2.26 (1.60), residues: 10 loop : -0.74 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.010 0.001 PHE A 247 TYR 0.013 0.001 TYR A 444 ARG 0.001 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.385 Fit side-chains REVERT: A 44 GLU cc_start: 0.8160 (tp30) cc_final: 0.7883 (tp30) outliers start: 13 outliers final: 8 residues processed: 83 average time/residue: 0.1187 time to fit residues: 12.6760 Evaluate side-chains 79 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3420 Z= 0.193 Angle : 0.542 6.933 4648 Z= 0.266 Chirality : 0.038 0.141 544 Planarity : 0.003 0.030 567 Dihedral : 3.886 32.008 459 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.03 % Allowed : 36.60 % Favored : 59.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.43), residues: 424 helix: 2.78 (0.29), residues: 325 sheet: -2.36 (1.56), residues: 10 loop : -0.77 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.003 0.001 HIS A 348 PHE 0.009 0.001 PHE A 194 TYR 0.012 0.001 TYR A 444 ARG 0.000 0.000 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.372 Fit side-chains REVERT: A 44 GLU cc_start: 0.8194 (tp30) cc_final: 0.7907 (tp30) REVERT: A 117 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7939 (mpp) REVERT: A 192 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7292 (ttp80) outliers start: 14 outliers final: 10 residues processed: 83 average time/residue: 0.1342 time to fit residues: 14.1638 Evaluate side-chains 84 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 0.0000 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN A 528 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3420 Z= 0.187 Angle : 0.557 7.083 4648 Z= 0.269 Chirality : 0.039 0.203 544 Planarity : 0.003 0.029 567 Dihedral : 3.905 33.068 459 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.32 % Allowed : 37.46 % Favored : 58.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.43), residues: 424 helix: 2.78 (0.29), residues: 325 sheet: -2.59 (1.48), residues: 10 loop : -0.80 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.009 0.001 PHE A 194 TYR 0.012 0.001 TYR A 444 ARG 0.000 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.390 Fit side-chains REVERT: A 44 GLU cc_start: 0.8153 (tp30) cc_final: 0.7885 (tp30) REVERT: A 117 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7850 (mmp) REVERT: A 192 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7297 (ttp80) outliers start: 15 outliers final: 10 residues processed: 82 average time/residue: 0.1295 time to fit residues: 13.3837 Evaluate side-chains 83 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 452 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 35 optimal weight: 0.0170 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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: 0.8012 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3420 Z= 0.178 Angle : 0.569 7.315 4648 Z= 0.273 Chirality : 0.039 0.140 544 Planarity : 0.003 0.029 567 Dihedral : 3.889 33.436 459 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.19 % Allowed : 36.31 % Favored : 58.50 % 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: 3.00 (0.43), residues: 424 helix: 2.83 (0.29), residues: 325 sheet: -2.63 (1.47), residues: 10 loop : -0.82 (0.70), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 368 HIS 0.002 0.000 HIS A 348 PHE 0.009 0.001 PHE A 240 TYR 0.012 0.001 TYR A 444 ARG 0.000 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.375 Fit side-chains REVERT: A 44 GLU cc_start: 0.8152 (tp30) cc_final: 0.7927 (tp30) REVERT: A 117 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7704 (mmp) REVERT: A 192 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7273 (ttp80) REVERT: A 311 LYS cc_start: 0.6009 (OUTLIER) cc_final: 0.5405 (pttp) outliers start: 18 outliers final: 9 residues processed: 86 average time/residue: 0.1333 time to fit residues: 14.3560 Evaluate side-chains 81 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.0370 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.0770 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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: 0.8001 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3420 Z= 0.168 Angle : 0.570 7.525 4648 Z= 0.273 Chirality : 0.039 0.141 544 Planarity : 0.003 0.029 567 Dihedral : 3.905 33.466 459 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.75 % Allowed : 37.46 % Favored : 58.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.43), residues: 424 helix: 2.82 (0.29), residues: 325 sheet: -2.61 (1.47), residues: 10 loop : -0.81 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 368 HIS 0.002 0.000 HIS A 348 PHE 0.008 0.001 PHE A 194 TYR 0.014 0.001 TYR A 444 ARG 0.001 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.347 Fit side-chains REVERT: A 44 GLU cc_start: 0.8161 (tp30) cc_final: 0.7946 (tp30) REVERT: A 117 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7698 (mmp) REVERT: A 192 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7265 (ttp80) outliers start: 13 outliers final: 9 residues processed: 83 average time/residue: 0.1325 time to fit residues: 13.8105 Evaluate side-chains 86 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 466 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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: 0.7992 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3420 Z= 0.176 Angle : 0.588 7.871 4648 Z= 0.281 Chirality : 0.039 0.141 544 Planarity : 0.003 0.029 567 Dihedral : 3.899 33.719 459 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.75 % Allowed : 37.75 % Favored : 58.50 % 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: 3.00 (0.43), residues: 424 helix: 2.83 (0.29), residues: 325 sheet: -2.62 (1.47), residues: 10 loop : -0.78 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 368 HIS 0.002 0.000 HIS A 348 PHE 0.009 0.001 PHE A 240 TYR 0.013 0.001 TYR A 444 ARG 0.001 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.304 Fit side-chains REVERT: A 117 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7771 (mmp) REVERT: A 192 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7272 (ttp80) outliers start: 13 outliers final: 11 residues processed: 82 average time/residue: 0.1332 time to fit residues: 13.6644 Evaluate side-chains 88 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 452 TRP Chi-restraints excluded: chain A residue 466 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 23 optimal weight: 0.3980 chunk 16 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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: 0.7985 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3420 Z= 0.172 Angle : 0.575 7.884 4648 Z= 0.276 Chirality : 0.038 0.140 544 Planarity : 0.003 0.029 567 Dihedral : 3.895 33.749 459 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.90 % Allowed : 36.60 % Favored : 58.50 % 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: 3.05 (0.43), residues: 424 helix: 2.86 (0.29), residues: 325 sheet: -2.58 (1.48), residues: 10 loop : -0.77 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 368 HIS 0.002 0.000 HIS A 348 PHE 0.009 0.001 PHE A 240 TYR 0.013 0.001 TYR A 444 ARG 0.001 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.382 Fit side-chains REVERT: A 117 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7789 (mmp) REVERT: A 192 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7303 (ttp80) outliers start: 17 outliers final: 10 residues processed: 87 average time/residue: 0.1442 time to fit residues: 15.4849 Evaluate side-chains 89 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 452 TRP Chi-restraints excluded: chain A residue 466 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 0.0970 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.7994 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3420 Z= 0.190 Angle : 0.580 7.891 4648 Z= 0.281 Chirality : 0.039 0.140 544 Planarity : 0.003 0.029 567 Dihedral : 3.883 34.089 459 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.75 % Allowed : 36.89 % Favored : 59.37 % 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: 3.01 (0.43), residues: 424 helix: 2.86 (0.29), residues: 324 sheet: -2.62 (1.47), residues: 10 loop : -0.85 (0.71), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 368 HIS 0.002 0.000 HIS A 348 PHE 0.009 0.001 PHE A 240 TYR 0.013 0.001 TYR A 444 ARG 0.000 0.000 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.374 Fit side-chains REVERT: A 192 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7311 (ttp80) REVERT: A 489 MET cc_start: 0.8558 (ttm) cc_final: 0.8301 (tpp) outliers start: 13 outliers final: 11 residues processed: 85 average time/residue: 0.1427 time to fit residues: 15.0763 Evaluate side-chains 87 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 452 TRP Chi-restraints excluded: chain A residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8018 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3420 Z= 0.219 Angle : 0.616 7.846 4648 Z= 0.295 Chirality : 0.039 0.138 544 Planarity : 0.003 0.029 567 Dihedral : 3.906 34.967 459 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.46 % Allowed : 38.04 % Favored : 58.50 % 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: 2.88 (0.43), residues: 424 helix: 2.77 (0.29), residues: 324 sheet: -2.74 (1.42), residues: 10 loop : -0.90 (0.71), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.010 0.001 PHE A 194 TYR 0.012 0.001 TYR A 444 ARG 0.001 0.000 ARG A 404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.375 Fit side-chains REVERT: A 163 LEU cc_start: 0.8434 (tp) cc_final: 0.8172 (tp) REVERT: A 192 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7330 (ttp80) REVERT: A 489 MET cc_start: 0.8593 (ttm) cc_final: 0.8336 (tpp) outliers start: 12 outliers final: 10 residues processed: 81 average time/residue: 0.1380 time to fit residues: 13.9460 Evaluate side-chains 84 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 452 TRP Chi-restraints excluded: chain A residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.153122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125936 restraints weight = 5309.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.129594 restraints weight = 2939.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131838 restraints weight = 2086.904| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3420 Z= 0.226 Angle : 0.608 7.680 4648 Z= 0.297 Chirality : 0.039 0.139 544 Planarity : 0.003 0.029 567 Dihedral : 3.926 35.201 459 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.46 % Allowed : 38.04 % Favored : 58.50 % 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: 2.91 (0.43), residues: 424 helix: 2.79 (0.29), residues: 324 sheet: -2.77 (1.41), residues: 10 loop : -0.91 (0.71), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.010 0.001 PHE A 194 TYR 0.012 0.001 TYR A 444 ARG 0.001 0.000 ARG A 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1149.82 seconds wall clock time: 21 minutes 36.77 seconds (1296.77 seconds total)