Starting phenix.real_space_refine on Fri Aug 2 13:52:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/08_2024/8wll_37623.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/08_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_37623/08_2024/8wll_37623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/08_2024/8wll_37623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/08_2024/8wll_37623.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wll_37623/08_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-5409/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: 2.61, per 1000 atoms: 0.93 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: 1.25 Conformation dependent library (CDL) restraints added in 547.5 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: 0.24 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: 0.75 Time building geometry restraints manager: 1.25 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 3.040 nonbonded pdb=" O PHE A 170 " pdb=" OG1 THR A 173 " model vdw 2.281 3.040 nonbonded pdb=" O ALA A 297 " pdb=" OG SER A 300 " model vdw 2.295 3.040 nonbonded pdb=" OG SER A 325 " pdb=" OE1 GLN A 329 " model vdw 2.314 3.040 ... (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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.310 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- 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 : 0.278 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: 0.1042 time to fit residues: 18.5960 Evaluate side-chains 111 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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: 0.9990 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7752 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2883 Z= 0.254 Angle : 0.808 8.596 3943 Z= 0.382 Chirality : 0.045 0.188 486 Planarity : 0.006 0.054 479 Dihedral : 7.041 52.654 467 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.24 % Allowed : 19.42 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.44), residues: 385 helix: 1.09 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.98 (0.76), 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 0.002 PHE A 27 TYR 0.022 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 155 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 0.298 Fit side-chains REVERT: A 124 LEU cc_start: 0.7629 (tt) cc_final: 0.6912 (mp) REVERT: A 133 LEU cc_start: 0.8371 (mm) cc_final: 0.8048 (mm) REVERT: A 388 ASN cc_start: 0.8752 (m-40) cc_final: 0.8536 (m110) REVERT: A 408 TYR cc_start: 0.8283 (t80) cc_final: 0.7761 (t80) outliers start: 9 outliers final: 7 residues processed: 148 average time/residue: 0.0981 time to fit residues: 18.3077 Evaluate side-chains 121 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 186 LEU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.0050 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2883 Z= 0.246 Angle : 0.791 7.584 3943 Z= 0.376 Chirality : 0.045 0.193 486 Planarity : 0.005 0.039 479 Dihedral : 6.304 52.922 467 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.60 % Allowed : 25.90 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.44), residues: 385 helix: 1.19 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.94 (0.81), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 451 HIS 0.002 0.000 HIS A 353 PHE 0.019 0.001 PHE A 27 TYR 0.013 0.001 TYR A 341 ARG 0.001 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 : 0.330 Fit side-chains REVERT: A 124 LEU cc_start: 0.7668 (tt) cc_final: 0.7054 (mp) REVERT: A 133 LEU cc_start: 0.8410 (mm) cc_final: 0.8063 (mm) REVERT: A 388 ASN cc_start: 0.8740 (m-40) cc_final: 0.8463 (m110) REVERT: A 408 TYR cc_start: 0.8268 (t80) cc_final: 0.7785 (t80) outliers start: 10 outliers final: 7 residues processed: 142 average time/residue: 0.1126 time to fit residues: 20.3604 Evaluate side-chains 136 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 186 LEU 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 375 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.0170 chunk 36 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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: 0.7748 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 2883 Z= 0.235 Angle : 0.778 6.383 3943 Z= 0.369 Chirality : 0.045 0.185 486 Planarity : 0.005 0.038 479 Dihedral : 5.930 52.479 467 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.32 % Allowed : 26.62 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.44), residues: 385 helix: 1.28 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -3.01 (0.82), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 451 HIS 0.002 0.000 HIS A 353 PHE 0.019 0.001 PHE A 27 TYR 0.013 0.001 TYR A 341 ARG 0.001 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 152 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 0.303 Fit side-chains REVERT: A 124 LEU cc_start: 0.7694 (tt) cc_final: 0.7038 (mp) REVERT: A 133 LEU cc_start: 0.8392 (mm) cc_final: 0.8026 (mm) REVERT: A 191 LEU cc_start: 0.7851 (tt) cc_final: 0.7567 (tt) REVERT: A 230 MET cc_start: 0.8303 (ppp) cc_final: 0.7974 (tmm) REVERT: A 388 ASN cc_start: 0.8705 (m-40) cc_final: 0.8385 (m110) REVERT: A 408 TYR cc_start: 0.8258 (t80) cc_final: 0.7791 (t80) REVERT: A 453 MET cc_start: 0.8206 (mmm) cc_final: 0.7819 (mmm) outliers start: 12 outliers final: 8 residues processed: 144 average time/residue: 0.0979 time to fit residues: 17.8781 Evaluate side-chains 133 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 338 SER 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: 3.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.0040 chunk 21 optimal weight: 0.8980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 2883 Z= 0.240 Angle : 0.788 7.395 3943 Z= 0.375 Chirality : 0.045 0.193 486 Planarity : 0.005 0.038 479 Dihedral : 5.880 53.560 467 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.96 % Allowed : 29.86 % Favored : 66.19 % 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: 1.13 (0.44), residues: 385 helix: 1.32 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -2.90 (0.83), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.002 0.000 HIS A 353 PHE 0.019 0.001 PHE A 27 TYR 0.014 0.001 TYR A 341 ARG 0.000 0.000 ARG A 19 *********************** 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 148 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 0.329 Fit side-chains REVERT: A 49 TYR cc_start: 0.8052 (t80) cc_final: 0.7655 (t80) REVERT: A 124 LEU cc_start: 0.7678 (tt) cc_final: 0.7035 (mp) REVERT: A 133 LEU cc_start: 0.8390 (mm) cc_final: 0.8020 (mm) REVERT: A 152 LEU cc_start: 0.8812 (tp) cc_final: 0.8549 (tt) REVERT: A 191 LEU cc_start: 0.7945 (tt) cc_final: 0.7643 (tt) REVERT: A 230 MET cc_start: 0.8222 (ppp) cc_final: 0.7839 (tmm) REVERT: A 408 TYR cc_start: 0.8272 (t80) cc_final: 0.7794 (t80) REVERT: A 453 MET cc_start: 0.8238 (mmm) cc_final: 0.7825 (mmm) outliers start: 11 outliers final: 10 residues processed: 142 average time/residue: 0.1027 time to fit residues: 18.5736 Evaluate side-chains 145 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 186 LEU 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 324 CYS Chi-restraints excluded: chain A residue 338 SER 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: 0.0870 chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 192 GLN A 305 ASN A 388 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2883 Z= 0.240 Angle : 0.803 9.208 3943 Z= 0.383 Chirality : 0.045 0.182 486 Planarity : 0.004 0.038 479 Dihedral : 5.774 52.574 467 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.32 % Allowed : 33.09 % Favored : 62.59 % 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: 1.13 (0.44), residues: 385 helix: 1.31 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -2.86 (0.85), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 451 HIS 0.006 0.002 HIS A 53 PHE 0.019 0.001 PHE A 27 TYR 0.015 0.001 TYR A 341 ARG 0.000 0.000 ARG A 357 *********************** 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 133 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 0.302 Fit side-chains REVERT: A 49 TYR cc_start: 0.8022 (t80) cc_final: 0.7656 (t80) REVERT: A 133 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7812 (tp) REVERT: A 169 MET cc_start: 0.8973 (tpp) cc_final: 0.8754 (tpp) REVERT: A 191 LEU cc_start: 0.7993 (tt) cc_final: 0.7671 (tt) REVERT: A 315 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8408 (mp) REVERT: A 327 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7715 (mtmm) REVERT: A 388 ASN cc_start: 0.8638 (m-40) cc_final: 0.8405 (m110) REVERT: A 408 TYR cc_start: 0.8272 (t80) cc_final: 0.7795 (t80) REVERT: A 453 MET cc_start: 0.8215 (mmm) cc_final: 0.7840 (mmm) outliers start: 12 outliers final: 8 residues processed: 129 average time/residue: 0.0999 time to fit residues: 16.2655 Evaluate side-chains 144 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 186 LEU 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 451 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.0040 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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: 0.7745 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 2883 Z= 0.241 Angle : 0.829 11.804 3943 Z= 0.394 Chirality : 0.046 0.180 486 Planarity : 0.005 0.038 479 Dihedral : 5.800 51.944 467 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.40 % Allowed : 32.01 % Favored : 62.59 % 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 (0.44), residues: 385 helix: 1.24 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -2.82 (0.86), residues: 52 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 0.012 0.001 TYR A 341 ARG 0.001 0.000 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 149 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.287 Fit side-chains REVERT: A 49 TYR cc_start: 0.8052 (t80) cc_final: 0.7720 (t80) REVERT: A 124 LEU cc_start: 0.7731 (tt) cc_final: 0.7113 (mp) REVERT: A 133 LEU cc_start: 0.8397 (mm) cc_final: 0.8031 (mm) REVERT: A 152 LEU cc_start: 0.8780 (tp) cc_final: 0.8502 (tt) REVERT: A 191 LEU cc_start: 0.7966 (tt) cc_final: 0.7645 (tt) REVERT: A 230 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7869 (tmm) REVERT: A 327 LYS cc_start: 0.7952 (ttmm) cc_final: 0.7662 (mtmm) REVERT: A 341 TYR cc_start: 0.8075 (t80) cc_final: 0.7646 (t80) REVERT: A 388 ASN cc_start: 0.8667 (m-40) cc_final: 0.8422 (m110) REVERT: A 408 TYR cc_start: 0.8272 (t80) cc_final: 0.7796 (t80) REVERT: A 453 MET cc_start: 0.8200 (mmm) cc_final: 0.7850 (mmm) outliers start: 15 outliers final: 9 residues processed: 144 average time/residue: 0.1013 time to fit residues: 18.5003 Evaluate side-chains 133 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 186 LEU 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 338 SER Chi-restraints excluded: chain A residue 421 VAL 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: 0.0010 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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: 0.7758 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 2883 Z= 0.248 Angle : 0.851 10.156 3943 Z= 0.403 Chirality : 0.047 0.204 486 Planarity : 0.005 0.037 479 Dihedral : 5.685 51.953 467 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.32 % Allowed : 34.17 % Favored : 61.51 % 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: 0.92 (0.44), residues: 385 helix: 1.19 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.93 (0.83), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.008 0.002 HIS A 53 PHE 0.018 0.001 PHE A 27 TYR 0.016 0.001 TYR A 341 ARG 0.001 0.000 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 135 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 0.302 Fit side-chains REVERT: A 49 TYR cc_start: 0.8098 (t80) cc_final: 0.7769 (t80) REVERT: A 133 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7853 (tp) REVERT: A 191 LEU cc_start: 0.8014 (tt) cc_final: 0.7707 (tt) REVERT: A 327 LYS cc_start: 0.7996 (ttmm) cc_final: 0.7659 (mtmm) REVERT: A 388 ASN cc_start: 0.8683 (m-40) cc_final: 0.8383 (m110) REVERT: A 408 TYR cc_start: 0.8280 (t80) cc_final: 0.7799 (t80) REVERT: A 453 MET cc_start: 0.8237 (mmm) cc_final: 0.7897 (mmm) outliers start: 12 outliers final: 10 residues processed: 131 average time/residue: 0.1004 time to fit residues: 16.7626 Evaluate side-chains 145 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 186 LEU 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 324 CYS 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: 0.7980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 chunk 23 optimal weight: 0.0370 chunk 18 optimal weight: 0.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2871 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= 0.247 Angle : 0.887 13.968 3943 Z= 0.416 Chirality : 0.048 0.210 486 Planarity : 0.005 0.035 479 Dihedral : 5.760 52.193 467 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.68 % Allowed : 35.97 % 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: 0.85 (0.44), residues: 385 helix: 1.14 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -2.96 (0.83), residues: 53 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 0.018 0.001 PHE A 27 TYR 0.014 0.001 TYR A 211 ARG 0.001 0.000 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 142 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 0.280 Fit side-chains REVERT: A 49 TYR cc_start: 0.8075 (t80) cc_final: 0.7745 (t80) REVERT: A 124 LEU cc_start: 0.7764 (tt) cc_final: 0.7187 (mp) REVERT: A 133 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8034 (mm) REVERT: A 191 LEU cc_start: 0.7982 (tt) cc_final: 0.7680 (tt) REVERT: A 230 MET cc_start: 0.8248 (ppp) cc_final: 0.7818 (tmm) REVERT: A 327 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7656 (mtmm) REVERT: A 388 ASN cc_start: 0.8692 (m-40) cc_final: 0.8388 (m110) REVERT: A 408 TYR cc_start: 0.8281 (t80) cc_final: 0.7796 (t80) REVERT: A 453 MET cc_start: 0.8211 (mmm) cc_final: 0.7882 (mmm) outliers start: 13 outliers final: 11 residues processed: 135 average time/residue: 0.0993 time to fit residues: 17.1577 Evaluate side-chains 139 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 338 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 23 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.0040 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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: 0.7764 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 2883 Z= 0.262 Angle : 0.883 13.205 3943 Z= 0.417 Chirality : 0.048 0.211 486 Planarity : 0.005 0.034 479 Dihedral : 5.719 51.904 467 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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: 0.81 (0.44), residues: 385 helix: 1.12 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -3.10 (0.84), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.007 0.002 HIS A 53 PHE 0.022 0.001 PHE A 303 TYR 0.015 0.002 TYR A 211 ARG 0.001 0.000 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 143 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 0.333 Fit side-chains REVERT: A 49 TYR cc_start: 0.8099 (t80) cc_final: 0.7779 (t80) REVERT: A 124 LEU cc_start: 0.7763 (tt) cc_final: 0.7191 (mp) REVERT: A 133 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8036 (mm) REVERT: A 175 MET cc_start: 0.7678 (mtp) cc_final: 0.7341 (mtp) REVERT: A 191 LEU cc_start: 0.8010 (tt) cc_final: 0.7713 (tt) REVERT: A 327 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7617 (mtmm) REVERT: A 388 ASN cc_start: 0.8697 (m-40) cc_final: 0.8384 (m110) REVERT: A 408 TYR cc_start: 0.8285 (t80) cc_final: 0.7797 (t80) REVERT: A 453 MET cc_start: 0.8262 (mmm) cc_final: 0.7887 (mmm) outliers start: 12 outliers final: 10 residues processed: 137 average time/residue: 0.1028 time to fit residues: 17.8203 Evaluate side-chains 140 residues out of total 315 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 324 CYS 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: 0.7980 chunk 1 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.0010 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.146048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128321 restraints weight = 5250.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.131915 restraints weight = 3091.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.134344 restraints weight = 2057.464| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 2883 Z= 0.259 Angle : 0.887 12.917 3943 Z= 0.420 Chirality : 0.048 0.211 486 Planarity : 0.005 0.035 479 Dihedral : 5.726 52.204 467 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.04 % Allowed : 37.05 % Favored : 57.91 % 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: 1.07 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -3.15 (0.83), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.007 0.002 HIS A 53 PHE 0.022 0.001 PHE A 463 TYR 0.016 0.002 TYR A 211 ARG 0.001 0.000 ARG A 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1043.42 seconds wall clock time: 19 minutes 1.11 seconds (1141.11 seconds total)