Starting phenix.real_space_refine on Mon Feb 10 21:37:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wll_37623/02_2025/8wll_37623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wll_37623/02_2025/8wll_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/cci-nas-00/data/ceres_data/8wll_37623/02_2025/8wll_37623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wll_37623/02_2025/8wll_37623.map" model { file = "/net/cci-nas-00/data/ceres_data/8wll_37623/02_2025/8wll_37623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wll_37623/02_2025/8wll_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. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 2.63, 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 - 3.00 Amino acid : True - 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: 0.84 Conformation dependent library (CDL) restraints added in 384.7 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: 0.76 Time building geometry restraints manager: 0.95 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: 0.00 - 2.20: 3768 2.20 - 4.40: 119 4.40 - 6.60: 41 6.60 - 8.80: 10 8.80 - 11.00: 5 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: 0.730 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.250 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.050 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.302 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: 0.1166 time to fit residues: 20.8544 Evaluate side-chains 111 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128191 restraints weight = 5235.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.131762 restraints weight = 3200.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.134144 restraints weight = 2168.819| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 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 to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.308 Fit side-chains REVERT: A 124 LEU cc_start: 0.7694 (tt) cc_final: 0.6939 (mp) REVERT: A 133 LEU cc_start: 0.8401 (mm) cc_final: 0.8066 (mm) REVERT: A 355 MET cc_start: 0.7990 (ppp) cc_final: 0.7780 (ppp) REVERT: A 388 ASN cc_start: 0.8741 (m-40) cc_final: 0.8506 (m110) REVERT: A 402 MET cc_start: 0.8254 (mmp) cc_final: 0.8046 (mmp) REVERT: A 408 TYR cc_start: 0.8325 (t80) cc_final: 0.7758 (t80) outliers start: 9 outliers final: 7 residues processed: 148 average time/residue: 0.1019 time to fit residues: 19.0395 Evaluate side-chains 121 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 34 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.124386 restraints weight = 5243.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127883 restraints weight = 3146.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.130505 restraints weight = 2113.620| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 2883 Z= 0.291 Angle : 0.787 7.626 3943 Z= 0.379 Chirality : 0.045 0.165 486 Planarity : 0.005 0.042 479 Dihedral : 6.271 53.022 467 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.32 % Allowed : 26.26 % Favored : 69.42 % 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: 1.12 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -2.88 (0.81), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.019 0.001 PHE A 27 TYR 0.014 0.002 TYR A 47 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 149 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 49 TYR cc_start: 0.8161 (t80) cc_final: 0.7736 (t80) REVERT: A 330 LEU cc_start: 0.7421 (mt) cc_final: 0.6834 (mt) REVERT: A 355 MET cc_start: 0.7959 (ppp) cc_final: 0.7756 (tmm) REVERT: A 388 ASN cc_start: 0.8782 (m-40) cc_final: 0.8483 (m110) REVERT: A 408 TYR cc_start: 0.8320 (t80) cc_final: 0.7808 (t80) outliers start: 12 outliers final: 9 residues processed: 141 average time/residue: 0.1027 time to fit residues: 18.2994 Evaluate side-chains 135 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 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 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 34 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.142507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.124121 restraints weight = 5297.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127599 restraints weight = 3184.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.129853 restraints weight = 2143.857| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2365 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= 0.282 Angle : 0.800 7.091 3943 Z= 0.382 Chirality : 0.045 0.144 486 Planarity : 0.005 0.039 479 Dihedral : 6.094 52.293 467 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.68 % Allowed : 30.58 % Favored : 64.75 % 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: 333 sheet: None (None), residues: 0 loop : -2.96 (0.82), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.006 0.002 HIS A 53 PHE 0.020 0.001 PHE A 27 TYR 0.012 0.002 TYR A 47 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 138 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 49 TYR cc_start: 0.8128 (t80) cc_final: 0.7757 (t80) REVERT: A 191 LEU cc_start: 0.7984 (tt) cc_final: 0.7639 (tt) REVERT: A 330 LEU cc_start: 0.7458 (mt) cc_final: 0.6906 (mt) REVERT: A 388 ASN cc_start: 0.8818 (m-40) cc_final: 0.8500 (m110) REVERT: A 408 TYR cc_start: 0.8335 (t80) cc_final: 0.7812 (t80) REVERT: A 453 MET cc_start: 0.8385 (mmm) cc_final: 0.7871 (mmm) outliers start: 13 outliers final: 10 residues processed: 128 average time/residue: 0.1023 time to fit residues: 16.4737 Evaluate side-chains 137 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 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 300 SER Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 405 ILE 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 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.142890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.125382 restraints weight = 5282.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128956 restraints weight = 3090.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.131384 restraints weight = 2050.516| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2565 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= 0.253 Angle : 0.804 8.879 3943 Z= 0.383 Chirality : 0.044 0.153 486 Planarity : 0.005 0.039 479 Dihedral : 5.993 51.426 467 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.40 % Allowed : 28.78 % 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: 0.99 (0.44), residues: 385 helix: 1.23 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -2.96 (0.83), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.003 0.001 HIS A 53 PHE 0.019 0.001 PHE A 27 TYR 0.018 0.001 TYR A 47 ARG 0.001 0.000 ARG A 357 *********************** 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 142 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.321 Fit side-chains REVERT: A 191 LEU cc_start: 0.7998 (tt) cc_final: 0.7657 (tt) REVERT: A 315 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8611 (mp) REVERT: A 330 LEU cc_start: 0.7299 (mt) cc_final: 0.6749 (mt) REVERT: A 408 TYR cc_start: 0.8342 (t80) cc_final: 0.7803 (t80) REVERT: A 453 MET cc_start: 0.8357 (mmm) cc_final: 0.7855 (mmm) outliers start: 15 outliers final: 10 residues processed: 135 average time/residue: 0.1046 time to fit residues: 17.8575 Evaluate side-chains 135 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 255 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 338 SER Chi-restraints excluded: chain A residue 350 ILE 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 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.143104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125460 restraints weight = 5380.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129058 restraints weight = 3143.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.131717 restraints weight = 2078.390| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2672 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= 0.250 Angle : 0.806 8.892 3943 Z= 0.386 Chirality : 0.044 0.131 486 Planarity : 0.005 0.039 479 Dihedral : 5.946 51.297 467 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.47 % Allowed : 30.58 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.44), residues: 385 helix: 1.24 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -2.97 (0.85), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.006 0.002 HIS A 53 PHE 0.020 0.001 PHE A 27 TYR 0.012 0.001 TYR A 47 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 143 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.275 Fit side-chains REVERT: A 133 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7862 (tp) REVERT: A 175 MET cc_start: 0.7740 (mtp) cc_final: 0.7411 (mtp) REVERT: A 191 LEU cc_start: 0.7965 (tt) cc_final: 0.7619 (tt) REVERT: A 315 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8619 (mp) REVERT: A 341 TYR cc_start: 0.8102 (t80) cc_final: 0.7804 (t80) REVERT: A 388 ASN cc_start: 0.8796 (m-40) cc_final: 0.8570 (m110) REVERT: A 408 TYR cc_start: 0.8322 (t80) cc_final: 0.7787 (t80) REVERT: A 453 MET cc_start: 0.8322 (mmm) cc_final: 0.7849 (mmm) outliers start: 18 outliers final: 11 residues processed: 136 average time/residue: 0.0951 time to fit residues: 16.6470 Evaluate side-chains 138 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU 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 255 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 315 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 26 optimal weight: 0.0000 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.144127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126423 restraints weight = 5314.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130109 restraints weight = 3098.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.132645 restraints weight = 2037.370| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2793 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 : 0.829 10.653 3943 Z= 0.394 Chirality : 0.045 0.150 486 Planarity : 0.005 0.036 479 Dihedral : 5.941 52.026 467 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.47 % Allowed : 33.81 % Favored : 59.71 % 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: 1.18 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -2.96 (0.84), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.003 0.001 HIS A 53 PHE 0.019 0.001 PHE A 27 TYR 0.016 0.001 TYR A 47 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 141 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.292 Fit side-chains REVERT: A 133 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7879 (tp) REVERT: A 175 MET cc_start: 0.7860 (mtp) cc_final: 0.7525 (mtp) REVERT: A 191 LEU cc_start: 0.7971 (tt) cc_final: 0.7615 (tt) REVERT: A 315 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8593 (mp) REVERT: A 341 TYR cc_start: 0.8087 (t80) cc_final: 0.7752 (t80) REVERT: A 355 MET cc_start: 0.8075 (tmm) cc_final: 0.7714 (ppp) REVERT: A 388 ASN cc_start: 0.8772 (m-40) cc_final: 0.8510 (m110) REVERT: A 408 TYR cc_start: 0.8322 (t80) cc_final: 0.7762 (t80) REVERT: A 453 MET cc_start: 0.8345 (mmm) cc_final: 0.7857 (mmm) outliers start: 18 outliers final: 12 residues processed: 133 average time/residue: 0.1041 time to fit residues: 17.6200 Evaluate side-chains 137 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 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 255 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 315 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.143747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126372 restraints weight = 5216.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.129991 restraints weight = 3053.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.132440 restraints weight = 2013.370| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 2883 Z= 0.257 Angle : 0.851 14.372 3943 Z= 0.403 Chirality : 0.045 0.168 486 Planarity : 0.005 0.035 479 Dihedral : 5.976 51.892 467 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 6.47 % Allowed : 34.17 % 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: 0.88 (0.44), residues: 385 helix: 1.15 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -3.02 (0.83), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.003 0.001 HIS A 53 PHE 0.019 0.001 PHE A 27 TYR 0.010 0.001 TYR A 47 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 144 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.313 Fit side-chains REVERT: A 133 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7900 (tp) REVERT: A 191 LEU cc_start: 0.7976 (tt) cc_final: 0.7604 (tt) REVERT: A 248 LYS cc_start: 0.7692 (pttp) cc_final: 0.7471 (pttm) REVERT: A 315 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8598 (mp) REVERT: A 330 LEU cc_start: 0.7318 (mt) cc_final: 0.6916 (mt) REVERT: A 341 TYR cc_start: 0.8130 (t80) cc_final: 0.7682 (t80) REVERT: A 388 ASN cc_start: 0.8756 (m-40) cc_final: 0.8491 (m110) REVERT: A 408 TYR cc_start: 0.8328 (t80) cc_final: 0.7773 (t80) REVERT: A 453 MET cc_start: 0.8310 (mmm) cc_final: 0.7861 (mmm) outliers start: 18 outliers final: 14 residues processed: 137 average time/residue: 0.1012 time to fit residues: 17.6881 Evaluate side-chains 142 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 36 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 255 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 315 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 0.0040 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.145539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127597 restraints weight = 5229.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.131340 restraints weight = 3011.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.133907 restraints weight = 1976.108| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 2883 Z= 0.248 Angle : 0.867 13.176 3943 Z= 0.410 Chirality : 0.046 0.167 486 Planarity : 0.005 0.035 479 Dihedral : 5.931 52.382 467 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.76 % Allowed : 35.61 % Favored : 58.63 % 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: 333 sheet: None (None), residues: 0 loop : -3.03 (0.83), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 328 HIS 0.003 0.001 HIS A 53 PHE 0.018 0.001 PHE A 27 TYR 0.015 0.001 TYR A 47 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 149 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.311 Fit side-chains REVERT: A 124 LEU cc_start: 0.7801 (tt) cc_final: 0.7218 (mp) REVERT: A 133 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8047 (mm) REVERT: A 175 MET cc_start: 0.7867 (mtp) cc_final: 0.7546 (mtp) REVERT: A 191 LEU cc_start: 0.7882 (tt) cc_final: 0.7514 (tt) REVERT: A 341 TYR cc_start: 0.8061 (t80) cc_final: 0.7631 (t80) REVERT: A 388 ASN cc_start: 0.8713 (m-40) cc_final: 0.8392 (m110) REVERT: A 408 TYR cc_start: 0.8326 (t80) cc_final: 0.7747 (t80) REVERT: A 453 MET cc_start: 0.8327 (mmm) cc_final: 0.7890 (mmm) outliers start: 16 outliers final: 13 residues processed: 141 average time/residue: 0.0948 time to fit residues: 16.9242 Evaluate side-chains 145 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 36 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 315 LEU 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 24 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.144990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127160 restraints weight = 5298.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130841 restraints weight = 3067.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.133374 restraints weight = 2014.368| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 2883 Z= 0.269 Angle : 0.897 15.553 3943 Z= 0.423 Chirality : 0.048 0.197 486 Planarity : 0.005 0.036 479 Dihedral : 5.893 52.307 467 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.68 % Allowed : 38.49 % Favored : 56.83 % 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: 0.79 (0.44), residues: 385 helix: 1.10 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -3.16 (0.83), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.003 0.001 HIS A 53 PHE 0.023 0.001 PHE A 303 TYR 0.015 0.001 TYR A 341 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 to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.278 Fit side-chains REVERT: A 124 LEU cc_start: 0.7894 (tt) cc_final: 0.7327 (mp) REVERT: A 133 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8055 (mm) REVERT: A 175 MET cc_start: 0.7859 (mtp) cc_final: 0.7546 (mtp) REVERT: A 191 LEU cc_start: 0.7947 (tt) cc_final: 0.7581 (tt) REVERT: A 388 ASN cc_start: 0.8716 (m-40) cc_final: 0.8398 (m110) REVERT: A 408 TYR cc_start: 0.8332 (t80) cc_final: 0.7763 (t80) REVERT: A 453 MET cc_start: 0.8366 (mmm) cc_final: 0.7923 (mmm) outliers start: 13 outliers final: 12 residues processed: 137 average time/residue: 0.1031 time to fit residues: 18.0578 Evaluate side-chains 144 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 36 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 315 LEU 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 15 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.0470 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.145818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127918 restraints weight = 5141.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131517 restraints weight = 3035.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.134074 restraints weight = 2025.447| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3175 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= 0.254 Angle : 0.887 15.264 3943 Z= 0.420 Chirality : 0.048 0.205 486 Planarity : 0.005 0.036 479 Dihedral : 6.056 52.973 467 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.40 % Allowed : 38.85 % Favored : 55.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.44), residues: 385 helix: 1.08 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -3.16 (0.83), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 328 HIS 0.003 0.001 HIS A 53 PHE 0.022 0.001 PHE A 303 TYR 0.017 0.001 TYR A 341 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: 1182.04 seconds wall clock time: 22 minutes 18.27 seconds (1338.27 seconds total)