Starting phenix.real_space_refine on Thu Jul 18 18:54:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/07_2024/8jjo_36361_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/07_2024/8jjo_36361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/07_2024/8jjo_36361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/07_2024/8jjo_36361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/07_2024/8jjo_36361_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjo_36361/07_2024/8jjo_36361_neut.cif" } resolution = 3.4 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= 0.158 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 20 5.16 5 C 1980 2.51 5 N 487 2.21 5 O 529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 122": "OE1" <-> "OE2" Residue "F GLU 180": "OE1" <-> "OE2" Residue "F TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 238": "OE1" <-> "OE2" Residue "F ASP 242": "OD1" <-> "OD2" Residue "F ASP 296": "OD1" <-> "OD2" Residue "F TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 335": "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: 3016 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2998 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 8, 'TRANS': 366} Chain breaks: 1 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'JTZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.54, per 1000 atoms: 0.84 Number of scatterers: 3016 At special positions: 0 Unit cell: (54.57, 81.32, 107, 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 20 16.00 O 529 8.00 N 487 7.00 C 1980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 106 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 190 " distance=2.03 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: 1.40 Conformation dependent library (CDL) restraints added in 520.9 milliseconds 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 722 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'F' and resid 29 through 61 removed outlier: 3.703A pdb=" N VAL F 34 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY F 37 " --> pdb=" O VAL F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 86 Processing helix chain 'F' and resid 86 through 96 Processing helix chain 'F' and resid 106 through 134 Processing helix chain 'F' and resid 146 through 170 removed outlier: 4.093A pdb=" N LEU F 167 " --> pdb=" O LEU F 163 " (cutoff:3.500A) Proline residue: F 168 - end of helix Processing helix chain 'F' and resid 180 through 186 removed outlier: 3.816A pdb=" N ASN F 183 " --> pdb=" O GLU F 180 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA F 186 " --> pdb=" O ASN F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 207 Processing helix chain 'F' and resid 210 through 237 removed outlier: 3.560A pdb=" N VAL F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS F 227 " --> pdb=" O PHE F 223 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG F 228 " --> pdb=" O GLN F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 247 Processing helix chain 'F' and resid 252 through 273 Processing helix chain 'F' and resid 279 through 300 Processing helix chain 'F' and resid 309 through 366 removed outlier: 4.393A pdb=" N GLN F 326 " --> pdb=" O ASN F 322 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS F 340 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR F 350 " --> pdb=" O MET F 346 " (cutoff:3.500A) Proline residue: F 355 - end of helix removed outlier: 3.506A pdb=" N VAL F 359 " --> pdb=" O PRO F 355 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE F 361 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL F 362 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL F 364 " --> pdb=" O ASN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 386 removed outlier: 3.909A pdb=" N GLY F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER F 386 " --> pdb=" O GLY F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 394 removed outlier: 4.366A pdb=" N LEU F 391 " --> pdb=" O GLY F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 405 removed outlier: 3.525A pdb=" N ALA F 402 " --> pdb=" O ASP F 398 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.75 Time building geometry restraints manager: 1.42 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: 930 1.34 - 1.46: 738 1.46 - 1.58: 1384 1.58 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 3083 Sorted by residual: bond pdb=" C12 JTZ F 501 " pdb=" C7 JTZ F 501 " ideal model delta sigma weight residual 1.403 1.353 0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C2 JTZ F 501 " pdb=" N1 JTZ F 501 " ideal model delta sigma weight residual 1.458 1.417 0.041 2.00e-02 2.50e+03 4.14e+00 bond pdb=" C8 JTZ F 501 " pdb=" C9 JTZ F 501 " ideal model delta sigma weight residual 1.390 1.352 0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" C7 JTZ F 501 " pdb=" C8 JTZ F 501 " ideal model delta sigma weight residual 1.393 1.357 0.036 2.00e-02 2.50e+03 3.25e+00 bond pdb=" C10 JTZ F 501 " pdb=" C9 JTZ F 501 " ideal model delta sigma weight residual 1.385 1.351 0.034 2.00e-02 2.50e+03 2.88e+00 ... (remaining 3078 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.16: 52 106.16 - 113.11: 1689 113.11 - 120.06: 1100 120.06 - 127.01: 1311 127.01 - 133.95: 32 Bond angle restraints: 4184 Sorted by residual: angle pdb=" C1 JTZ F 501 " pdb=" C2 JTZ F 501 " pdb=" N1 JTZ F 501 " ideal model delta sigma weight residual 114.33 105.42 8.91 3.00e+00 1.11e-01 8.83e+00 angle pdb=" C2 JTZ F 501 " pdb=" N1 JTZ F 501 " pdb=" C4 JTZ F 501 " ideal model delta sigma weight residual 115.12 106.67 8.45 3.00e+00 1.11e-01 7.93e+00 angle pdb=" N TRP F 105 " pdb=" CA TRP F 105 " pdb=" C TRP F 105 " ideal model delta sigma weight residual 113.38 110.14 3.24 1.17e+00 7.31e-01 7.69e+00 angle pdb=" C ASP F 367 " pdb=" N ASN F 368 " pdb=" CA ASN F 368 " ideal model delta sigma weight residual 121.54 126.63 -5.09 1.91e+00 2.74e-01 7.09e+00 angle pdb=" C6 JTZ F 501 " pdb=" C5 JTZ F 501 " pdb=" O1 JTZ F 501 " ideal model delta sigma weight residual 112.06 104.46 7.60 3.00e+00 1.11e-01 6.42e+00 ... (remaining 4179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 1729 31.27 - 62.54: 83 62.54 - 93.82: 8 93.82 - 125.09: 0 125.09 - 156.36: 1 Dihedral angle restraints: 1821 sinusoidal: 713 harmonic: 1108 Sorted by residual: dihedral pdb=" CB CYS F 184 " pdb=" SG CYS F 184 " pdb=" SG CYS F 190 " pdb=" CB CYS F 190 " ideal model delta sinusoidal sigma weight residual -86.00 0.68 -86.68 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYS F 106 " pdb=" SG CYS F 106 " pdb=" SG CYS F 191 " pdb=" CB CYS F 191 " ideal model delta sinusoidal sigma weight residual -86.00 -162.86 76.86 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" C4 JTZ F 501 " pdb=" C5 JTZ F 501 " pdb=" C6 JTZ F 501 " pdb=" O2 JTZ F 501 " ideal model delta sinusoidal sigma weight residual 181.12 24.76 156.36 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 1818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 430 0.060 - 0.120: 56 0.120 - 0.181: 1 0.181 - 0.241: 0 0.241 - 0.301: 1 Chirality restraints: 488 Sorted by residual: chirality pdb=" C5 JTZ F 501 " pdb=" C4 JTZ F 501 " pdb=" C6 JTZ F 501 " pdb=" O1 JTZ F 501 " both_signs ideal model delta sigma weight residual False -2.33 -2.63 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB ILE F 370 " pdb=" CA ILE F 370 " pdb=" CG1 ILE F 370 " pdb=" CG2 ILE F 370 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ASN F 368 " pdb=" N ASN F 368 " pdb=" C ASN F 368 " pdb=" CB ASN F 368 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.22e-01 ... (remaining 485 not shown) Planarity restraints: 513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 237 " 0.003 2.00e-02 2.50e+03 8.53e-03 1.82e+00 pdb=" CG TRP F 237 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP F 237 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP F 237 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 237 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP F 237 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 237 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 237 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 237 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 237 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 385 " 0.006 2.00e-02 2.50e+03 1.10e-02 1.22e+00 pdb=" C ASN F 385 " -0.019 2.00e-02 2.50e+03 pdb=" O ASN F 385 " 0.007 2.00e-02 2.50e+03 pdb=" N SER F 386 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 354 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO F 355 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO F 355 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 355 " -0.015 5.00e-02 4.00e+02 ... (remaining 510 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 140 2.73 - 3.27: 3211 3.27 - 3.81: 5027 3.81 - 4.36: 5604 4.36 - 4.90: 9744 Nonbonded interactions: 23726 Sorted by model distance: nonbonded pdb=" OH TYR F 219 " pdb=" O LEU F 339 " model vdw 2.184 2.440 nonbonded pdb=" OD2 ASP F 113 " pdb=" OH TYR F 383 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR F 118 " pdb=" OG SER F 207 " model vdw 2.276 2.440 nonbonded pdb=" O ALA F 119 " pdb=" OG1 THR F 123 " model vdw 2.377 2.440 nonbonded pdb=" C4 JTZ F 501 " pdb=" O2 JTZ F 501 " model vdw 2.378 2.752 ... (remaining 23721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 0.020 Set scattering table: 0.030 Process input model: 13.440 Find NCS groups from input model: 0.020 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 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 0.050 3083 Z= 0.234 Angle : 0.637 8.912 4184 Z= 0.328 Chirality : 0.041 0.301 488 Planarity : 0.003 0.027 513 Dihedral : 17.699 156.361 1093 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.31 % Allowed : 17.96 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.44), residues: 371 helix: 0.85 (0.31), residues: 293 sheet: None (None), residues: 0 loop : -3.64 (0.54), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 237 HIS 0.006 0.001 HIS F 286 PHE 0.007 0.001 PHE F 193 TYR 0.010 0.001 TYR F 383 ARG 0.004 0.000 ARG F 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.332 Fit side-chains REVERT: F 171 MET cc_start: 0.6084 (ppp) cc_final: 0.5567 (ppp) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.1092 time to fit residues: 7.6025 Evaluate side-chains 54 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 223 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 326 GLN F 360 ASN ** F 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3083 Z= 0.250 Angle : 0.551 6.646 4184 Z= 0.290 Chirality : 0.040 0.124 488 Planarity : 0.003 0.025 513 Dihedral : 8.968 127.775 409 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.02 % Allowed : 17.65 % Favored : 78.33 % 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: 0.35 (0.45), residues: 371 helix: 1.06 (0.31), residues: 302 sheet: None (None), residues: 0 loop : -3.51 (0.61), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 237 HIS 0.004 0.001 HIS F 286 PHE 0.009 0.001 PHE F 356 TYR 0.019 0.002 TYR F 383 ARG 0.003 0.000 ARG F 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.347 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 63 average time/residue: 0.0869 time to fit residues: 7.3524 Evaluate side-chains 58 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 386 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.0670 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3083 Z= 0.196 Angle : 0.503 7.726 4184 Z= 0.266 Chirality : 0.038 0.107 488 Planarity : 0.003 0.028 513 Dihedral : 8.474 117.226 409 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.72 % Allowed : 20.43 % Favored : 75.85 % 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: 0.46 (0.45), residues: 371 helix: 1.20 (0.31), residues: 298 sheet: None (None), residues: 0 loop : -3.50 (0.57), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 380 HIS 0.003 0.001 HIS F 286 PHE 0.006 0.001 PHE F 356 TYR 0.014 0.001 TYR F 383 ARG 0.002 0.000 ARG F 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.315 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 65 average time/residue: 0.0928 time to fit residues: 8.1748 Evaluate side-chains 59 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 374 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3083 Z= 0.174 Angle : 0.508 9.990 4184 Z= 0.260 Chirality : 0.037 0.104 488 Planarity : 0.003 0.029 513 Dihedral : 8.213 112.718 409 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.64 % Allowed : 21.05 % Favored : 74.30 % 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: 0.62 (0.45), residues: 371 helix: 1.31 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.88 (0.54), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 380 HIS 0.002 0.001 HIS F 286 PHE 0.007 0.001 PHE F 288 TYR 0.010 0.001 TYR F 383 ARG 0.002 0.000 ARG F 371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 0.318 Fit side-chains REVERT: F 257 LYS cc_start: 0.7832 (ttmt) cc_final: 0.7434 (ttmt) outliers start: 15 outliers final: 11 residues processed: 66 average time/residue: 0.1050 time to fit residues: 8.8914 Evaluate side-chains 64 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 374 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.0010 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 20 optimal weight: 6.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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: 0.6816 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3083 Z= 0.161 Angle : 0.492 9.251 4184 Z= 0.253 Chirality : 0.036 0.105 488 Planarity : 0.003 0.030 513 Dihedral : 7.884 109.099 409 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.64 % Allowed : 22.60 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.46), residues: 371 helix: 1.38 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.90 (0.53), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 380 HIS 0.002 0.001 HIS F 178 PHE 0.008 0.001 PHE F 49 TYR 0.011 0.001 TYR F 383 ARG 0.002 0.000 ARG F 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.279 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 68 average time/residue: 0.1067 time to fit residues: 9.4696 Evaluate side-chains 62 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 374 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.6847 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3083 Z= 0.187 Angle : 0.512 9.555 4184 Z= 0.261 Chirality : 0.037 0.107 488 Planarity : 0.003 0.029 513 Dihedral : 7.776 108.583 409 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.72 % Allowed : 24.77 % Favored : 71.52 % 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: 0.72 (0.46), residues: 371 helix: 1.36 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.81 (0.53), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 380 HIS 0.002 0.001 HIS F 178 PHE 0.009 0.001 PHE F 288 TYR 0.027 0.002 TYR F 174 ARG 0.002 0.000 ARG F 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.345 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 66 average time/residue: 0.0997 time to fit residues: 8.7885 Evaluate side-chains 65 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 374 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3083 Z= 0.171 Angle : 0.506 9.325 4184 Z= 0.257 Chirality : 0.037 0.116 488 Planarity : 0.003 0.031 513 Dihedral : 7.691 107.208 409 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.47 % Favored : 93.26 % Rotamer: Outliers : 4.33 % Allowed : 24.46 % Favored : 71.21 % 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: 0.78 (0.46), residues: 371 helix: 1.40 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.81 (0.54), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 380 HIS 0.001 0.001 HIS F 286 PHE 0.008 0.001 PHE F 49 TYR 0.023 0.002 TYR F 174 ARG 0.001 0.000 ARG F 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.304 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 63 average time/residue: 0.0843 time to fit residues: 7.2236 Evaluate side-chains 67 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 374 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3083 Z= 0.176 Angle : 0.509 9.634 4184 Z= 0.258 Chirality : 0.037 0.111 488 Planarity : 0.003 0.031 513 Dihedral : 7.682 107.506 409 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.28 % Favored : 92.45 % Rotamer: Outliers : 4.95 % Allowed : 24.15 % Favored : 70.90 % 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: 0.81 (0.46), residues: 371 helix: 1.43 (0.31), residues: 305 sheet: None (None), residues: 0 loop : -3.88 (0.53), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 380 HIS 0.001 0.000 HIS F 178 PHE 0.008 0.001 PHE F 49 TYR 0.022 0.002 TYR F 174 ARG 0.001 0.000 ARG F 371 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.292 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 64 average time/residue: 0.0953 time to fit residues: 8.1351 Evaluate side-chains 67 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 374 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 30 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 51 ASN F 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3083 Z= 0.220 Angle : 0.542 8.942 4184 Z= 0.278 Chirality : 0.038 0.115 488 Planarity : 0.003 0.029 513 Dihedral : 7.774 109.535 409 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.20 % Favored : 93.53 % Rotamer: Outliers : 4.33 % Allowed : 24.77 % Favored : 70.90 % 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: 0.70 (0.45), residues: 371 helix: 1.36 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.86 (0.51), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 380 HIS 0.001 0.000 HIS F 178 PHE 0.009 0.001 PHE F 288 TYR 0.020 0.002 TYR F 174 ARG 0.002 0.000 ARG F 371 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.339 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 65 average time/residue: 0.0929 time to fit residues: 8.0962 Evaluate side-chains 66 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 374 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 363 HIS F 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3083 Z= 0.241 Angle : 0.558 9.576 4184 Z= 0.283 Chirality : 0.038 0.115 488 Planarity : 0.003 0.029 513 Dihedral : 7.859 110.508 409 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.47 % Favored : 93.26 % Rotamer: Outliers : 4.64 % Allowed : 25.39 % Favored : 69.97 % 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: 0.63 (0.45), residues: 371 helix: 1.28 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -3.68 (0.52), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 99 HIS 0.001 0.001 HIS F 178 PHE 0.009 0.001 PHE F 288 TYR 0.020 0.002 TYR F 174 ARG 0.001 0.000 ARG F 321 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.302 Fit side-chains REVERT: F 257 LYS cc_start: 0.7725 (ttmt) cc_final: 0.7327 (ttmt) outliers start: 15 outliers final: 14 residues processed: 67 average time/residue: 0.0957 time to fit residues: 8.5933 Evaluate side-chains 67 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 325 ILE Chi-restraints excluded: chain F residue 341 THR Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 374 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 363 HIS F 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.213071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.168298 restraints weight = 3479.192| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.37 r_work: 0.3984 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3083 Z= 0.228 Angle : 0.563 9.670 4184 Z= 0.286 Chirality : 0.039 0.116 488 Planarity : 0.003 0.029 513 Dihedral : 7.892 109.720 409 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.39 % Favored : 94.34 % Rotamer: Outliers : 4.33 % Allowed : 26.63 % Favored : 69.04 % 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: 0.83 (0.45), residues: 371 helix: 1.46 (0.31), residues: 295 sheet: None (None), residues: 0 loop : -3.21 (0.54), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 380 HIS 0.001 0.001 HIS F 178 PHE 0.008 0.001 PHE F 193 TYR 0.020 0.002 TYR F 174 ARG 0.001 0.000 ARG F 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 974.97 seconds wall clock time: 21 minutes 26.22 seconds (1286.22 seconds total)