Starting phenix.real_space_refine on Thu Jul 18 19:50:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3e_41859/07_2024/8u3e_41859.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3e_41859/07_2024/8u3e_41859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3e_41859/07_2024/8u3e_41859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3e_41859/07_2024/8u3e_41859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3e_41859/07_2024/8u3e_41859.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3e_41859/07_2024/8u3e_41859.cif" } resolution = 3.19 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= 0.004 sd= 0.073 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 15 5.16 5 C 2230 2.51 5 N 522 2.21 5 O 571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3338 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3338 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain breaks: 1 Time building chain proxies: 3.08, per 1000 atoms: 0.92 Number of scatterers: 3338 At special positions: 0 Unit cell: (62.25, 76.36, 81.34, 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 15 16.00 O 571 8.00 N 522 7.00 C 2230 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: 1.34 Conformation dependent library (CDL) restraints added in 601.8 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 37 through 68 removed outlier: 3.502A pdb=" N PHE A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.621A pdb=" N GLN A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 124 through 134 removed outlier: 3.706A pdb=" N TYR A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 158 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 161 through 176 Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.787A pdb=" N ALA A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 224 removed outlier: 3.736A pdb=" N SER A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 226 through 247 removed outlier: 4.026A pdb=" N PHE A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 259 through 276 removed outlier: 4.886A pdb=" N ASN A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 319 removed outlier: 3.518A pdb=" N TRP A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 332 through 356 removed outlier: 4.178A pdb=" N GLY A 346 " --> pdb=" O MET A 342 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 360 removed outlier: 3.707A pdb=" N THR A 360 " --> pdb=" O ASN A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 361 through 385 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.509A pdb=" N GLY A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.919A pdb=" N ASP A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 removed outlier: 4.096A pdb=" N GLY A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 447 removed outlier: 3.577A pdb=" N MET A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 4.007A pdb=" N LYS A 445 " --> pdb=" O PRO A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 478 removed outlier: 4.113A pdb=" N THR A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) 233 hydrogen bonds defined for protein. 684 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: 0.95 Time building geometry restraints manager: 1.48 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: 982 1.34 - 1.46: 937 1.46 - 1.58: 1497 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3440 Sorted by residual: bond pdb=" N LEU A 45 " pdb=" CA LEU A 45 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.28e-02 6.10e+03 6.70e+00 bond pdb=" N THR A 107 " pdb=" CA THR A 107 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.17e+00 bond pdb=" N GLN A 123 " pdb=" CA GLN A 123 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.24e-02 6.50e+03 6.13e+00 bond pdb=" N ILE A 44 " pdb=" CA ILE A 44 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.37e-02 5.33e+03 5.86e+00 bond pdb=" CA VAL A 482 " pdb=" CB VAL A 482 " ideal model delta sigma weight residual 1.553 1.536 0.017 7.40e-03 1.83e+04 5.21e+00 ... (remaining 3435 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.75: 64 105.75 - 112.83: 1834 112.83 - 119.91: 1174 119.91 - 126.99: 1564 126.99 - 134.07: 58 Bond angle restraints: 4694 Sorted by residual: angle pdb=" N LEU A 45 " pdb=" CA LEU A 45 " pdb=" C LEU A 45 " ideal model delta sigma weight residual 113.88 107.58 6.30 1.23e+00 6.61e-01 2.63e+01 angle pdb=" N ILE A 44 " pdb=" CA ILE A 44 " pdb=" C ILE A 44 " ideal model delta sigma weight residual 112.83 107.84 4.99 9.90e-01 1.02e+00 2.55e+01 angle pdb=" N SER A 420 " pdb=" CA SER A 420 " pdb=" CB SER A 420 " ideal model delta sigma weight residual 114.17 110.82 3.35 1.14e+00 7.69e-01 8.64e+00 angle pdb=" C MET A 372 " pdb=" N ILE A 373 " pdb=" CA ILE A 373 " ideal model delta sigma weight residual 122.66 119.85 2.81 9.70e-01 1.06e+00 8.40e+00 angle pdb=" N ALA A 43 " pdb=" CA ALA A 43 " pdb=" C ALA A 43 " ideal model delta sigma weight residual 113.18 109.84 3.34 1.21e+00 6.83e-01 7.62e+00 ... (remaining 4689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.67: 1694 14.67 - 29.34: 192 29.34 - 44.01: 44 44.01 - 58.68: 4 58.68 - 73.35: 3 Dihedral angle restraints: 1937 sinusoidal: 716 harmonic: 1221 Sorted by residual: dihedral pdb=" CA GLN A 483 " pdb=" C GLN A 483 " pdb=" N ASN A 484 " pdb=" CA ASN A 484 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA TYR A 389 " pdb=" C TYR A 389 " pdb=" N SER A 390 " pdb=" CA SER A 390 " ideal model delta harmonic sigma weight residual -180.00 -163.80 -16.20 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA LEU A 476 " pdb=" C LEU A 476 " pdb=" N PHE A 477 " pdb=" CA PHE A 477 " ideal model delta harmonic sigma weight residual -180.00 -164.76 -15.24 0 5.00e+00 4.00e-02 9.30e+00 ... (remaining 1934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 271 0.032 - 0.064: 163 0.064 - 0.096: 79 0.096 - 0.128: 18 0.128 - 0.160: 2 Chirality restraints: 533 Sorted by residual: chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA PRO A 252 " pdb=" N PRO A 252 " pdb=" C PRO A 252 " pdb=" CB PRO A 252 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 530 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 289 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO A 290 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 214 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.22e+00 pdb=" N PRO A 215 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 124 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 125 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.015 5.00e-02 4.00e+02 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1052 2.80 - 3.33: 3348 3.33 - 3.85: 5581 3.85 - 4.38: 6639 4.38 - 4.90: 11494 Nonbonded interactions: 28114 Sorted by model distance: nonbonded pdb=" OH TYR A 101 " pdb=" OD1 ASP A 158 " model vdw 2.280 2.440 nonbonded pdb=" OH TYR A 40 " pdb=" OE2 GLU A 194 " model vdw 2.286 2.440 nonbonded pdb=" O SER A 213 " pdb=" OG SER A 217 " model vdw 2.371 2.440 nonbonded pdb=" O THR A 397 " pdb=" OG1 THR A 401 " model vdw 2.379 2.440 nonbonded pdb=" O THR A 448 " pdb=" OG1 THR A 448 " model vdw 2.380 2.440 ... (remaining 28109 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: 1.130 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.000 Find NCS groups from input model: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 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 : 0.009 0.048 3440 Z= 0.564 Angle : 0.694 6.305 4694 Z= 0.416 Chirality : 0.047 0.160 533 Planarity : 0.004 0.033 569 Dihedral : 13.042 73.345 1161 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % 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: -3.53 (0.34), residues: 423 helix: -1.91 (0.24), residues: 330 sheet: None (None), residues: 0 loop : -3.21 (0.51), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 244 HIS 0.004 0.001 HIS A 414 PHE 0.016 0.001 PHE A 232 TYR 0.014 0.001 TYR A 261 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.415 Fit side-chains REVERT: A 66 ASP cc_start: 0.7642 (t70) cc_final: 0.7035 (t0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1251 time to fit residues: 3.5905 Evaluate side-chains 18 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3440 Z= 0.210 Angle : 0.555 5.502 4694 Z= 0.291 Chirality : 0.043 0.160 533 Planarity : 0.005 0.043 569 Dihedral : 4.397 14.436 455 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.57 % Allowed : 9.38 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.41), residues: 423 helix: -0.00 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -2.18 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 103 HIS 0.002 0.000 HIS A 414 PHE 0.018 0.001 PHE A 232 TYR 0.011 0.001 TYR A 335 ARG 0.001 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.343 Fit side-chains REVERT: A 66 ASP cc_start: 0.7392 (t70) cc_final: 0.7045 (t0) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.1857 time to fit residues: 5.3904 Evaluate side-chains 20 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7940 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3440 Z= 0.190 Angle : 0.512 5.061 4694 Z= 0.269 Chirality : 0.042 0.144 533 Planarity : 0.005 0.044 569 Dihedral : 4.210 13.803 455 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.42 % Allowed : 10.80 % Favored : 87.78 % 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: 0.04 (0.43), residues: 423 helix: 0.58 (0.30), residues: 337 sheet: None (None), residues: 0 loop : -1.97 (0.65), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 103 HIS 0.002 0.000 HIS A 255 PHE 0.013 0.001 PHE A 232 TYR 0.011 0.001 TYR A 335 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.354 Fit side-chains REVERT: A 66 ASP cc_start: 0.7691 (t70) cc_final: 0.7243 (t0) REVERT: A 256 LYS cc_start: 0.8158 (mtmm) cc_final: 0.7792 (mtmm) outliers start: 5 outliers final: 2 residues processed: 26 average time/residue: 0.1700 time to fit residues: 5.6615 Evaluate side-chains 24 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.0020 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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: 0.7975 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3440 Z= 0.194 Angle : 0.519 5.088 4694 Z= 0.270 Chirality : 0.042 0.141 533 Planarity : 0.005 0.045 569 Dihedral : 4.164 13.004 455 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.70 % Allowed : 11.93 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.42), residues: 423 helix: 0.79 (0.30), residues: 337 sheet: None (None), residues: 0 loop : -1.78 (0.63), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 356 HIS 0.002 0.000 HIS A 255 PHE 0.011 0.001 PHE A 232 TYR 0.010 0.001 TYR A 335 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.340 Fit side-chains REVERT: A 66 ASP cc_start: 0.7919 (t70) cc_final: 0.7418 (t0) REVERT: A 185 MET cc_start: 0.8789 (mtp) cc_final: 0.8577 (mtp) REVERT: A 256 LYS cc_start: 0.8210 (mtmm) cc_final: 0.7843 (mtmm) outliers start: 6 outliers final: 3 residues processed: 28 average time/residue: 0.1514 time to fit residues: 5.5797 Evaluate side-chains 26 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 450 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8020 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3440 Z= 0.222 Angle : 0.533 5.166 4694 Z= 0.277 Chirality : 0.042 0.139 533 Planarity : 0.005 0.046 569 Dihedral : 4.195 13.372 455 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.99 % Allowed : 14.20 % Favored : 83.81 % 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: 0.68 (0.42), residues: 423 helix: 0.97 (0.30), residues: 333 sheet: None (None), residues: 0 loop : -1.30 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 356 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE A 299 TYR 0.012 0.001 TYR A 335 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.275 Fit side-chains REVERT: A 66 ASP cc_start: 0.8108 (t70) cc_final: 0.7570 (t0) REVERT: A 256 LYS cc_start: 0.8241 (mtmm) cc_final: 0.7922 (mtmm) outliers start: 7 outliers final: 5 residues processed: 29 average time/residue: 0.1701 time to fit residues: 6.2163 Evaluate side-chains 29 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 24 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 450 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 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: 0.7989 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3440 Z= 0.170 Angle : 0.514 5.152 4694 Z= 0.265 Chirality : 0.041 0.138 533 Planarity : 0.005 0.046 569 Dihedral : 4.113 13.769 455 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.56 % Allowed : 14.49 % Favored : 82.95 % 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: 0.89 (0.43), residues: 423 helix: 1.16 (0.30), residues: 333 sheet: None (None), residues: 0 loop : -1.40 (0.65), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 103 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE A 299 TYR 0.010 0.001 TYR A 335 ARG 0.005 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 24 time to evaluate : 0.271 Fit side-chains REVERT: A 66 ASP cc_start: 0.8120 (t70) cc_final: 0.7591 (t0) REVERT: A 256 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7954 (mtmm) outliers start: 9 outliers final: 6 residues processed: 30 average time/residue: 0.1416 time to fit residues: 5.6457 Evaluate side-chains 30 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 450 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.0980 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.7986 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3440 Z= 0.168 Angle : 0.511 5.679 4694 Z= 0.263 Chirality : 0.041 0.138 533 Planarity : 0.005 0.046 569 Dihedral : 4.065 13.328 455 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.27 % Allowed : 14.77 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.43), residues: 423 helix: 1.30 (0.30), residues: 332 sheet: None (None), residues: 0 loop : -1.56 (0.62), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 103 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE A 299 TYR 0.010 0.001 TYR A 335 ARG 0.004 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 25 time to evaluate : 0.345 Fit side-chains REVERT: A 256 LYS cc_start: 0.8284 (mtmm) cc_final: 0.7961 (mtmm) outliers start: 8 outliers final: 6 residues processed: 30 average time/residue: 0.1488 time to fit residues: 5.8688 Evaluate side-chains 30 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7993 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3440 Z= 0.183 Angle : 0.519 5.218 4694 Z= 0.269 Chirality : 0.041 0.199 533 Planarity : 0.005 0.046 569 Dihedral : 4.095 13.443 455 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.27 % Allowed : 15.34 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.43), residues: 423 helix: 1.29 (0.30), residues: 333 sheet: None (None), residues: 0 loop : -1.59 (0.62), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 103 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE A 299 TYR 0.010 0.001 TYR A 335 ARG 0.003 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.345 Fit side-chains REVERT: A 256 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7962 (mtmm) outliers start: 8 outliers final: 7 residues processed: 31 average time/residue: 0.1750 time to fit residues: 6.8151 Evaluate side-chains 32 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 450 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3440 Z= 0.196 Angle : 0.527 5.250 4694 Z= 0.274 Chirality : 0.042 0.217 533 Planarity : 0.005 0.046 569 Dihedral : 4.110 13.889 455 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.99 % Allowed : 15.62 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.43), residues: 423 helix: 1.28 (0.30), residues: 334 sheet: None (None), residues: 0 loop : -1.52 (0.62), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 103 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE A 299 TYR 0.011 0.001 TYR A 335 ARG 0.004 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 0.338 Fit side-chains REVERT: A 256 LYS cc_start: 0.8280 (mtmm) cc_final: 0.7959 (mtmm) outliers start: 7 outliers final: 7 residues processed: 30 average time/residue: 0.1799 time to fit residues: 6.8109 Evaluate side-chains 32 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 450 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7997 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3440 Z= 0.181 Angle : 0.521 5.219 4694 Z= 0.271 Chirality : 0.041 0.186 533 Planarity : 0.005 0.046 569 Dihedral : 4.090 13.955 455 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.27 % Allowed : 15.62 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.43), residues: 423 helix: 1.33 (0.30), residues: 333 sheet: None (None), residues: 0 loop : -1.57 (0.62), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 103 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE A 299 TYR 0.010 0.001 TYR A 335 ARG 0.004 0.000 ARG A 321 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 25 time to evaluate : 0.330 Fit side-chains REVERT: A 256 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7956 (mtmm) outliers start: 8 outliers final: 7 residues processed: 30 average time/residue: 0.1561 time to fit residues: 5.9142 Evaluate side-chains 32 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 450 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.0970 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.138247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113770 restraints weight = 4175.456| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.98 r_work: 0.3260 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3440 Z= 0.165 Angle : 0.509 5.691 4694 Z= 0.264 Chirality : 0.041 0.192 533 Planarity : 0.005 0.046 569 Dihedral : 4.041 13.850 455 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.27 % Allowed : 15.34 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.43), residues: 423 helix: 1.32 (0.30), residues: 339 sheet: None (None), residues: 0 loop : -1.41 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 103 HIS 0.001 0.000 HIS A 414 PHE 0.011 0.001 PHE A 299 TYR 0.009 0.001 TYR A 335 ARG 0.004 0.000 ARG A 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1111.88 seconds wall clock time: 22 minutes 0.42 seconds (1320.42 seconds total)