Starting phenix.real_space_refine on Thu Jul 18 18:23:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/07_2024/8wll_37623.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/07_2024/8wll_37623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/07_2024/8wll_37623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/07_2024/8wll_37623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/07_2024/8wll_37623.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/07_2024/8wll_37623.cif" } resolution = 3.74 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= 0.000 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 1875 2.51 5 N 433 2.21 5 O 479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 433": "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: 2815 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2771 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 22, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 108 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.44, per 1000 atoms: 0.87 Number of scatterers: 2815 At special positions: 0 Unit cell: (73.216, 53.248, 64.064, 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 28 16.00 O 479 8.00 N 433 7.00 C 1875 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: 1.78 Conformation dependent library (CDL) restraints added in 550.9 milliseconds 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 702 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 89.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 18 through 40 removed outlier: 3.847A pdb=" N ILE A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 54 removed outlier: 3.625A pdb=" N GLU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 156 removed outlier: 4.112A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.942A pdb=" N ILE A 162 " --> pdb=" O TYR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 removed outlier: 3.822A pdb=" N ILE A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N MET A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 removed outlier: 4.161A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.540A pdb=" N VAL A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 270 removed outlier: 3.518A pdb=" N LEU A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 291 through 321 removed outlier: 3.784A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 328 through 349 removed outlier: 4.544A pdb=" N VAL A 332 " --> pdb=" O TRP A 328 " (cutoff:3.500A) Proline residue: A 336 - end of helix Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 384 through 414 Proline residue: A 404 - end of helix removed outlier: 3.998A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 447 Proline residue: A 437 - end of helix removed outlier: 4.142A pdb=" N ALA A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 243 hydrogen bonds defined for protein. 717 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: 0.67 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.87: 2 0.87 - 1.10: 0 1.10 - 1.34: 842 1.34 - 1.58: 1987 1.58 - 1.82: 52 Bond restraints: 2883 Sorted by residual: bond pdb=" C6 YHR A 501 " pdb=" C7 YHR A 501 " ideal model delta sigma weight residual 1.521 0.629 0.892 2.00e-02 2.50e+03 1.99e+03 bond pdb=" C13 YHR A 501 " pdb=" C14 YHR A 501 " ideal model delta sigma weight residual 1.527 0.839 0.688 2.00e-02 2.50e+03 1.18e+03 bond pdb=" C5 YHR A 501 " pdb=" C6 YHR A 501 " ideal model delta sigma weight residual 1.527 1.276 0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C12 YHR A 501 " pdb=" C13 YHR A 501 " ideal model delta sigma weight residual 1.503 1.745 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C16 YHR A 501 " pdb=" C3 YHR A 501 " ideal model delta sigma weight residual 1.531 1.299 0.232 2.00e-02 2.50e+03 1.34e+02 ... (remaining 2878 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.36: 104 106.36 - 113.26: 1570 113.26 - 120.17: 1085 120.17 - 127.07: 1150 127.07 - 133.97: 34 Bond angle restraints: 3943 Sorted by residual: angle pdb=" CB MET A 397 " pdb=" CG MET A 397 " pdb=" SD MET A 397 " ideal model delta sigma weight residual 112.70 123.70 -11.00 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C7 YHR A 501 " pdb=" N8 YHR A 501 " pdb=" C9 YHR A 501 " ideal model delta sigma weight residual 111.89 122.57 -10.68 3.00e+00 1.11e-01 1.27e+01 angle pdb=" C33 YHR A 501 " pdb=" C31 YHR A 501 " pdb=" O30 YHR A 501 " ideal model delta sigma weight residual 112.77 122.76 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" N GLY A 235 " pdb=" CA GLY A 235 " pdb=" C GLY A 235 " ideal model delta sigma weight residual 112.34 118.82 -6.48 2.04e+00 2.40e-01 1.01e+01 angle pdb=" CB MET A 403 " pdb=" CG MET A 403 " pdb=" SD MET A 403 " ideal model delta sigma weight residual 112.70 121.92 -9.22 3.00e+00 1.11e-01 9.45e+00 ... (remaining 3938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.56: 1468 11.56 - 23.11: 147 23.11 - 34.66: 72 34.66 - 46.22: 27 46.22 - 57.77: 5 Dihedral angle restraints: 1719 sinusoidal: 619 harmonic: 1100 Sorted by residual: dihedral pdb=" CA ARG A 326 " pdb=" C ARG A 326 " pdb=" N LYS A 327 " pdb=" CA LYS A 327 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLY A 235 " pdb=" C GLY A 235 " pdb=" N PRO A 236 " pdb=" CA PRO A 236 " ideal model delta harmonic sigma weight residual -180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CG ARG A 357 " pdb=" CD ARG A 357 " pdb=" NE ARG A 357 " pdb=" CZ ARG A 357 " ideal model delta sinusoidal sigma weight residual 90.00 130.81 -40.81 2 1.50e+01 4.44e-03 9.11e+00 ... (remaining 1716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.348: 483 0.348 - 0.695: 1 0.695 - 1.043: 1 1.043 - 1.391: 0 1.391 - 1.738: 1 Chirality restraints: 486 Sorted by residual: chirality pdb=" C6 YHR A 501 " pdb=" C15 YHR A 501 " pdb=" C5 YHR A 501 " pdb=" C7 YHR A 501 " both_signs ideal model delta sigma weight residual False 2.53 0.79 1.74 2.00e-01 2.50e+01 7.55e+01 chirality pdb=" C13 YHR A 501 " pdb=" C12 YHR A 501 " pdb=" C14 YHR A 501 " pdb=" N8 YHR A 501 " both_signs ideal model delta sigma weight residual False -2.29 -1.46 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C3 YHR A 501 " pdb=" C16 YHR A 501 " pdb=" C4 YHR A 501 " pdb=" O2 YHR A 501 " both_signs ideal model delta sigma weight residual False 2.58 2.11 0.47 2.00e-01 2.50e+01 5.64e+00 ... (remaining 483 not shown) Planarity restraints: 479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 291 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO A 292 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 250 " -0.045 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO A 251 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 251 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 251 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 375 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A 376 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 376 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 376 " -0.028 5.00e-02 4.00e+02 ... (remaining 476 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 552 2.77 - 3.30: 3075 3.30 - 3.84: 4819 3.84 - 4.37: 5149 4.37 - 4.90: 9055 Nonbonded interactions: 22650 Sorted by model distance: nonbonded pdb=" C15 YHR A 501 " pdb=" N8 YHR A 501 " model vdw 2.238 2.840 nonbonded pdb=" OG SER A 137 " pdb=" OG SER A 190 " model vdw 2.268 2.440 nonbonded pdb=" O PHE A 170 " pdb=" OG1 THR A 173 " model vdw 2.281 2.440 nonbonded pdb=" O ALA A 297 " pdb=" OG SER A 300 " model vdw 2.295 2.440 nonbonded pdb=" OG SER A 325 " pdb=" OE1 GLN A 329 " model vdw 2.314 2.440 ... (remaining 22645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.080 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.024 0.892 2883 Z= 1.747 Angle : 1.058 11.003 3943 Z= 0.473 Chirality : 0.102 1.738 486 Planarity : 0.007 0.083 479 Dihedral : 13.070 57.774 1017 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.44), residues: 385 helix: 0.87 (0.30), residues: 323 sheet: None (None), residues: 0 loop : -1.89 (0.79), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.020 0.002 PHE A 166 TYR 0.016 0.002 TYR A 47 ARG 0.003 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.287 Fit side-chains REVERT: A 144 ILE cc_start: 0.8518 (mm) cc_final: 0.8285 (mm) REVERT: A 287 THR cc_start: 0.7984 (p) cc_final: 0.7783 (p) REVERT: A 408 TYR cc_start: 0.8277 (t80) cc_final: 0.7731 (t80) REVERT: A 453 MET cc_start: 0.7950 (mmm) cc_final: 0.7587 (mmm) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.0957 time to fit residues: 17.1068 Evaluate side-chains 111 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2883 Z= 0.250 Angle : 0.795 8.571 3943 Z= 0.374 Chirality : 0.045 0.184 486 Planarity : 0.006 0.054 479 Dihedral : 6.927 53.475 467 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.52 % Allowed : 20.86 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.44), residues: 385 helix: 1.07 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -3.01 (0.76), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.018 0.002 PHE A 27 TYR 0.021 0.002 TYR A 341 ARG 0.002 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 0.295 Fit side-chains REVERT: A 355 MET cc_start: 0.7910 (ppp) cc_final: 0.7703 (ppp) REVERT: A 408 TYR cc_start: 0.8286 (t80) cc_final: 0.7771 (t80) outliers start: 7 outliers final: 3 residues processed: 131 average time/residue: 0.1067 time to fit residues: 17.4399 Evaluate side-chains 118 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 380 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 2883 Z= 0.261 Angle : 0.778 6.397 3943 Z= 0.367 Chirality : 0.043 0.122 486 Planarity : 0.005 0.041 479 Dihedral : 6.254 53.964 467 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.60 % Allowed : 25.54 % Favored : 70.86 % 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: 0.90 (0.44), residues: 385 helix: 1.18 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.98 (0.77), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.019 0.001 PHE A 27 TYR 0.011 0.001 TYR A 47 ARG 0.002 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 0.295 Fit side-chains REVERT: A 124 LEU cc_start: 0.7669 (tt) cc_final: 0.7038 (mp) REVERT: A 133 LEU cc_start: 0.8391 (mm) cc_final: 0.8054 (mm) REVERT: A 230 MET cc_start: 0.8342 (ppp) cc_final: 0.8064 (tmm) REVERT: A 330 LEU cc_start: 0.7407 (mt) cc_final: 0.6800 (mt) REVERT: A 408 TYR cc_start: 0.8275 (t80) cc_final: 0.7806 (t80) REVERT: A 453 MET cc_start: 0.8289 (mmm) cc_final: 0.7893 (mmm) outliers start: 10 outliers final: 8 residues processed: 142 average time/residue: 0.1008 time to fit residues: 18.0477 Evaluate side-chains 128 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 380 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 2883 Z= 0.245 Angle : 0.790 7.286 3943 Z= 0.368 Chirality : 0.044 0.216 486 Planarity : 0.005 0.041 479 Dihedral : 6.319 53.567 467 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.04 % Allowed : 24.10 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.44), residues: 385 helix: 1.25 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -3.05 (0.77), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.001 0.000 HIS A 353 PHE 0.018 0.001 PHE A 27 TYR 0.012 0.001 TYR A 341 ARG 0.003 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 0.277 Fit side-chains REVERT: A 124 LEU cc_start: 0.7696 (tt) cc_final: 0.7023 (mp) REVERT: A 191 LEU cc_start: 0.8022 (tt) cc_final: 0.7737 (tt) REVERT: A 230 MET cc_start: 0.8360 (ppp) cc_final: 0.7996 (tmm) REVERT: A 285 LEU cc_start: 0.8316 (pt) cc_final: 0.8109 (pt) REVERT: A 330 LEU cc_start: 0.7338 (mt) cc_final: 0.6695 (mt) REVERT: A 408 TYR cc_start: 0.8270 (t80) cc_final: 0.7798 (t80) REVERT: A 453 MET cc_start: 0.8295 (mmm) cc_final: 0.7887 (mmm) outliers start: 14 outliers final: 9 residues processed: 139 average time/residue: 0.0941 time to fit residues: 16.5300 Evaluate side-chains 133 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 2883 Z= 0.254 Angle : 0.795 7.946 3943 Z= 0.371 Chirality : 0.044 0.176 486 Planarity : 0.004 0.041 479 Dihedral : 6.049 53.322 467 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.04 % Allowed : 29.14 % Favored : 65.83 % 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: 1.00 (0.44), residues: 385 helix: 1.24 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -2.94 (0.79), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.001 0.000 HIS A 353 PHE 0.019 0.001 PHE A 27 TYR 0.017 0.001 TYR A 47 ARG 0.003 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 0.293 Fit side-chains REVERT: A 191 LEU cc_start: 0.8136 (tt) cc_final: 0.7844 (tt) REVERT: A 315 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8574 (mp) REVERT: A 408 TYR cc_start: 0.8277 (t80) cc_final: 0.7796 (t80) REVERT: A 453 MET cc_start: 0.8256 (mmm) cc_final: 0.7875 (mmm) outliers start: 14 outliers final: 10 residues processed: 129 average time/residue: 0.0967 time to fit residues: 15.7206 Evaluate side-chains 134 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7805 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 2883 Z= 0.265 Angle : 0.803 9.892 3943 Z= 0.376 Chirality : 0.044 0.172 486 Planarity : 0.004 0.040 479 Dihedral : 5.938 52.642 467 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.68 % Allowed : 31.29 % Favored : 64.03 % 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: 0.96 (0.44), residues: 385 helix: 1.21 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -3.00 (0.80), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.009 0.002 HIS A 53 PHE 0.019 0.001 PHE A 27 TYR 0.014 0.001 TYR A 47 ARG 0.003 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.272 Fit side-chains REVERT: A 49 TYR cc_start: 0.8021 (t80) cc_final: 0.7621 (t80) REVERT: A 191 LEU cc_start: 0.8197 (tt) cc_final: 0.7912 (tt) REVERT: A 315 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8777 (mp) REVERT: A 408 TYR cc_start: 0.8293 (t80) cc_final: 0.7803 (t80) REVERT: A 453 MET cc_start: 0.8257 (mmm) cc_final: 0.7879 (mmm) outliers start: 13 outliers final: 11 residues processed: 129 average time/residue: 0.1009 time to fit residues: 16.5586 Evaluate side-chains 132 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 2883 Z= 0.256 Angle : 0.832 9.422 3943 Z= 0.390 Chirality : 0.045 0.150 486 Planarity : 0.004 0.039 479 Dihedral : 5.956 52.412 467 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.96 % Allowed : 34.89 % Favored : 61.15 % 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: 0.86 (0.44), residues: 385 helix: 1.14 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -2.98 (0.81), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.009 0.002 HIS A 53 PHE 0.018 0.001 PHE A 27 TYR 0.017 0.002 TYR A 211 ARG 0.003 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.302 Fit side-chains REVERT: A 191 LEU cc_start: 0.8148 (tt) cc_final: 0.7861 (tt) REVERT: A 315 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8542 (mp) REVERT: A 327 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7795 (mtmm) REVERT: A 408 TYR cc_start: 0.8291 (t80) cc_final: 0.7788 (t80) REVERT: A 453 MET cc_start: 0.8273 (mmm) cc_final: 0.7888 (mmm) outliers start: 11 outliers final: 10 residues processed: 128 average time/residue: 0.0986 time to fit residues: 15.9615 Evaluate side-chains 132 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 2883 Z= 0.257 Angle : 0.865 15.215 3943 Z= 0.403 Chirality : 0.046 0.159 486 Planarity : 0.004 0.039 479 Dihedral : 6.179 53.619 467 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.32 % Allowed : 36.69 % Favored : 58.99 % 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: 0.76 (0.44), residues: 385 helix: 1.06 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -3.07 (0.83), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.008 0.002 HIS A 53 PHE 0.019 0.001 PHE A 27 TYR 0.015 0.002 TYR A 211 ARG 0.003 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 0.309 Fit side-chains REVERT: A 43 ILE cc_start: 0.8627 (mt) cc_final: 0.8344 (mm) REVERT: A 191 LEU cc_start: 0.8132 (tt) cc_final: 0.7826 (tt) REVERT: A 315 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8754 (mp) REVERT: A 327 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7843 (mtmm) REVERT: A 408 TYR cc_start: 0.8295 (t80) cc_final: 0.7789 (t80) REVERT: A 453 MET cc_start: 0.8293 (mmm) cc_final: 0.7920 (mmm) outliers start: 12 outliers final: 10 residues processed: 128 average time/residue: 0.1002 time to fit residues: 16.5046 Evaluate side-chains 133 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 2883 Z= 0.254 Angle : 0.865 14.751 3943 Z= 0.404 Chirality : 0.045 0.160 486 Planarity : 0.004 0.039 479 Dihedral : 6.200 54.469 467 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.96 % Allowed : 38.49 % Favored : 57.55 % 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: 0.73 (0.44), residues: 385 helix: 1.05 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -3.06 (0.83), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.007 0.002 HIS A 53 PHE 0.017 0.001 PHE A 27 TYR 0.014 0.002 TYR A 341 ARG 0.004 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.219 Fit side-chains REVERT: A 43 ILE cc_start: 0.8594 (mt) cc_final: 0.8283 (mm) REVERT: A 191 LEU cc_start: 0.8116 (tt) cc_final: 0.7810 (tt) REVERT: A 211 TYR cc_start: 0.7773 (m-80) cc_final: 0.7558 (m-10) REVERT: A 315 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8535 (mp) REVERT: A 327 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7833 (mtmm) REVERT: A 408 TYR cc_start: 0.8294 (t80) cc_final: 0.7787 (t80) REVERT: A 453 MET cc_start: 0.8320 (mmm) cc_final: 0.7944 (mmm) outliers start: 11 outliers final: 8 residues processed: 129 average time/residue: 0.0949 time to fit residues: 15.3389 Evaluate side-chains 130 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.0050 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.0170 chunk 27 optimal weight: 0.0170 chunk 4 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 0.2670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 2883 Z= 0.241 Angle : 0.874 14.721 3943 Z= 0.406 Chirality : 0.045 0.158 486 Planarity : 0.004 0.039 479 Dihedral : 6.214 55.111 467 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.60 % Allowed : 38.13 % Favored : 58.27 % 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: 0.65 (0.44), residues: 385 helix: 1.02 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -3.16 (0.80), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 328 HIS 0.006 0.002 HIS A 53 PHE 0.023 0.001 PHE A 303 TYR 0.014 0.001 TYR A 211 ARG 0.004 0.001 ARG A 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 0.306 Fit side-chains REVERT: A 133 LEU cc_start: 0.8404 (mm) cc_final: 0.7850 (tp) REVERT: A 191 LEU cc_start: 0.7965 (tt) cc_final: 0.7655 (tt) REVERT: A 327 LYS cc_start: 0.8022 (ttmm) cc_final: 0.7725 (mtmm) REVERT: A 408 TYR cc_start: 0.8283 (t80) cc_final: 0.7771 (t80) REVERT: A 453 MET cc_start: 0.8229 (mmm) cc_final: 0.7903 (mmm) REVERT: A 463 PHE cc_start: 0.9125 (t80) cc_final: 0.8921 (t80) outliers start: 10 outliers final: 8 residues processed: 139 average time/residue: 0.0925 time to fit residues: 16.4572 Evaluate side-chains 143 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.145639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128393 restraints weight = 5189.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132070 restraints weight = 2988.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.134674 restraints weight = 1948.466| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 2883 Z= 0.267 Angle : 0.897 15.120 3943 Z= 0.418 Chirality : 0.047 0.216 486 Planarity : 0.005 0.038 479 Dihedral : 6.245 46.467 467 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.96 % Allowed : 36.69 % Favored : 59.35 % 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: 0.66 (0.44), residues: 385 helix: 0.99 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -3.06 (0.83), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.007 0.002 HIS A 53 PHE 0.026 0.001 PHE A 303 TYR 0.029 0.002 TYR A 341 ARG 0.002 0.000 ARG A 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 969.81 seconds wall clock time: 21 minutes 20.55 seconds (1280.55 seconds total)