Starting phenix.real_space_refine on Sat May 2 09:42:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ui1_64181/05_2026/9ui1_64181.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ui1_64181/05_2026/9ui1_64181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ui1_64181/05_2026/9ui1_64181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ui1_64181/05_2026/9ui1_64181.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ui1_64181/05_2026/9ui1_64181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ui1_64181/05_2026/9ui1_64181.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2811 2.51 5 N 657 2.21 5 O 725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4213 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4094 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 22, 'TRANS': 516} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 4, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 64 Chain: "A" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 119 Unusual residues: {'CLR': 1, 'POV': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-1': 6, 'POV:plan-2': 6, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 0.93, per 1000 atoms: 0.22 Number of scatterers: 4213 At special positions: 0 Unit cell: (85.85, 80.75, 73.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 725 8.00 N 657 7.00 C 2811 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: 0.29 Conformation dependent library (CDL) restraints added in 162.8 milliseconds 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 994 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 75.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 63 through 66 removed outlier: 4.156A pdb=" N LYS A 66 " --> pdb=" O ARG A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 67 through 80 removed outlier: 3.627A pdb=" N ILE A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 73 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASN A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 96 removed outlier: 3.863A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 129 removed outlier: 3.526A pdb=" N ALA A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE A 121 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 156 removed outlier: 3.737A pdb=" N ILE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.524A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 174 through 207 removed outlier: 3.539A pdb=" N ARG A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Proline residue: A 197 - end of helix removed outlier: 4.410A pdb=" N LEU A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA A 201 " --> pdb=" O PRO A 197 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 239 removed outlier: 3.646A pdb=" N PHE A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TRP A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 228 " --> pdb=" O TRP A 224 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 229 " --> pdb=" O TYR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 247 removed outlier: 3.568A pdb=" N SER A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 270 removed outlier: 4.271A pdb=" N ILE A 255 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Proline residue: A 256 - end of helix removed outlier: 3.622A pdb=" N GLY A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 298 removed outlier: 3.756A pdb=" N ILE A 287 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 358 through 389 removed outlier: 3.676A pdb=" N VAL A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix removed outlier: 4.108A pdb=" N ALA A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 399 removed outlier: 3.762A pdb=" N PHE A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 439 removed outlier: 4.027A pdb=" N MET A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Proline residue: A 436 - end of helix removed outlier: 3.837A pdb=" N ARG A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 449 through 482 removed outlier: 3.834A pdb=" N ARG A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 removed outlier: 3.632A pdb=" N TRP A 501 " --> pdb=" O SER A 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 502 through 528 removed outlier: 4.367A pdb=" N ILE A 518 " --> pdb=" O ALA A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 532 through 563 removed outlier: 4.137A pdb=" N PHE A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR A 541 " --> pdb=" O GLY A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 605 256 hydrogen bonds defined for protein. 762 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: 0.60 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 663 1.33 - 1.45: 1191 1.45 - 1.57: 2428 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 4316 Sorted by residual: bond pdb=" C ILE A 255 " pdb=" N PRO A 256 " ideal model delta sigma weight residual 1.335 1.364 -0.029 1.28e-02 6.10e+03 5.30e+00 bond pdb=" C MET A 68 " pdb=" N PRO A 69 " ideal model delta sigma weight residual 1.333 1.355 -0.021 1.44e-02 4.82e+03 2.21e+00 bond pdb=" CA VAL A 435 " pdb=" C VAL A 435 " ideal model delta sigma weight residual 1.520 1.532 -0.012 8.80e-03 1.29e+04 1.85e+00 bond pdb=" CA ILE A 372 " pdb=" C ILE A 372 " ideal model delta sigma weight residual 1.523 1.534 -0.010 9.20e-03 1.18e+04 1.28e+00 bond pdb=" C LYS A 301 " pdb=" O LYS A 301 " ideal model delta sigma weight residual 1.233 1.238 -0.005 4.80e-03 4.34e+04 1.24e+00 ... (remaining 4311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 5673 1.41 - 2.82: 149 2.82 - 4.23: 27 4.23 - 5.64: 6 5.64 - 7.05: 4 Bond angle restraints: 5859 Sorted by residual: angle pdb=" C VAL A 371 " pdb=" N ILE A 372 " pdb=" CA ILE A 372 " ideal model delta sigma weight residual 120.33 123.06 -2.73 8.00e-01 1.56e+00 1.17e+01 angle pdb=" C SER A 346 " pdb=" N ASP A 347 " pdb=" CA ASP A 347 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 angle pdb=" C PHE A 429 " pdb=" N TYR A 430 " pdb=" CA TYR A 430 " ideal model delta sigma weight residual 120.65 124.36 -3.71 1.32e+00 5.74e-01 7.92e+00 angle pdb=" C LEU A 300 " pdb=" N LYS A 301 " pdb=" CA LYS A 301 " ideal model delta sigma weight residual 123.10 125.80 -2.70 9.60e-01 1.09e+00 7.92e+00 angle pdb=" C ILE A 372 " pdb=" CA ILE A 372 " pdb=" CB ILE A 372 " ideal model delta sigma weight residual 114.00 110.33 3.67 1.31e+00 5.83e-01 7.85e+00 ... (remaining 5854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 2218 16.39 - 32.78: 245 32.78 - 49.17: 68 49.17 - 65.56: 12 65.56 - 81.95: 2 Dihedral angle restraints: 2545 sinusoidal: 990 harmonic: 1555 Sorted by residual: dihedral pdb=" CA PHE A 515 " pdb=" C PHE A 515 " pdb=" N ALA A 516 " pdb=" CA ALA A 516 " ideal model delta harmonic sigma weight residual -180.00 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA TYR A 129 " pdb=" C TYR A 129 " pdb=" N PHE A 130 " pdb=" CA PHE A 130 " ideal model delta harmonic sigma weight residual -180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA GLY A 73 " pdb=" C GLY A 73 " pdb=" N ASN A 74 " pdb=" CA ASN A 74 " ideal model delta harmonic sigma weight residual -180.00 -163.96 -16.04 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 2542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 432 0.029 - 0.057: 154 0.057 - 0.086: 65 0.086 - 0.115: 19 0.115 - 0.144: 7 Chirality restraints: 677 Sorted by residual: chirality pdb=" CA ASP A 347 " pdb=" N ASP A 347 " pdb=" C ASP A 347 " pdb=" CB ASP A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA VAL A 435 " pdb=" N VAL A 435 " pdb=" C VAL A 435 " pdb=" CB VAL A 435 " both_signs ideal model delta sigma weight residual False 2.44 2.31 0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA PRO A 353 " pdb=" N PRO A 353 " pdb=" C PRO A 353 " pdb=" CB PRO A 353 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 674 not shown) Planarity restraints: 715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 391 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.69e+00 pdb=" N PRO A 392 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 392 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 392 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 68 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO A 69 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 69 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 69 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 503 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO A 504 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 504 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 504 " 0.027 5.00e-02 4.00e+02 ... (remaining 712 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1225 2.81 - 3.34: 4197 3.34 - 3.86: 6445 3.86 - 4.38: 7186 4.38 - 4.90: 12466 Nonbonded interactions: 31519 Sorted by model distance: nonbonded pdb=" O PHE A 267 " pdb=" OH TYR A 274 " model vdw 2.293 3.040 nonbonded pdb=" ND2 ASN A 345 " pdb=" O SER A 351 " model vdw 2.301 3.120 nonbonded pdb=" O PHE A 376 " pdb=" OG1 THR A 379 " model vdw 2.308 3.040 nonbonded pdb=" O THR A 379 " pdb=" OG SER A 547 " model vdw 2.350 3.040 nonbonded pdb=" OG1 THR A 85 " pdb=" OD1 ASN A 88 " model vdw 2.361 3.040 ... (remaining 31514 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: 2.240 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.950 Find NCS groups from input model: 0.020 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4316 Z= 0.152 Angle : 0.579 7.046 5859 Z= 0.327 Chirality : 0.038 0.144 677 Planarity : 0.005 0.069 715 Dihedral : 14.955 81.951 1551 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.24 % Allowed : 25.36 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.37), residues: 535 helix: 1.21 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.08 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 298 TYR 0.009 0.001 TYR A 274 PHE 0.016 0.001 PHE A 77 TRP 0.017 0.001 TRP A 307 HIS 0.002 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4316) covalent geometry : angle 0.57886 ( 5859) hydrogen bonds : bond 0.22704 ( 256) hydrogen bonds : angle 5.99457 ( 762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.098 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.0469 time to fit residues: 3.9229 Evaluate side-chains 61 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 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 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.151388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126572 restraints weight = 6656.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.129500 restraints weight = 3598.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131360 restraints weight = 2553.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.132147 restraints weight = 2106.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.133032 restraints weight = 1923.459| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4316 Z= 0.159 Angle : 0.561 7.029 5859 Z= 0.306 Chirality : 0.040 0.149 677 Planarity : 0.005 0.066 715 Dihedral : 8.483 55.847 712 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.62 % Allowed : 22.95 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.38), residues: 535 helix: 1.68 (0.29), residues: 343 sheet: None (None), residues: 0 loop : -1.22 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 298 TYR 0.011 0.001 TYR A 430 PHE 0.022 0.001 PHE A 229 TRP 0.009 0.001 TRP A 354 HIS 0.003 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4316) covalent geometry : angle 0.56058 ( 5859) hydrogen bonds : bond 0.07328 ( 256) hydrogen bonds : angle 4.41083 ( 762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.141 Fit side-chains REVERT: A 183 MET cc_start: 0.7977 (tmm) cc_final: 0.7732 (tmm) REVERT: A 575 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8752 (mm) outliers start: 15 outliers final: 10 residues processed: 72 average time/residue: 0.0513 time to fit residues: 5.1174 Evaluate side-chains 71 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 593 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 27 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.152753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.128060 restraints weight = 6604.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131003 restraints weight = 3530.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132871 restraints weight = 2491.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133782 restraints weight = 2050.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133782 restraints weight = 1854.719| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4316 Z= 0.133 Angle : 0.526 6.951 5859 Z= 0.282 Chirality : 0.040 0.140 677 Planarity : 0.005 0.070 715 Dihedral : 8.041 59.862 712 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.83 % Allowed : 22.71 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.38), residues: 535 helix: 1.86 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -1.28 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 298 TYR 0.010 0.001 TYR A 430 PHE 0.021 0.001 PHE A 229 TRP 0.009 0.001 TRP A 354 HIS 0.002 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4316) covalent geometry : angle 0.52587 ( 5859) hydrogen bonds : bond 0.06230 ( 256) hydrogen bonds : angle 4.07968 ( 762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.118 Fit side-chains REVERT: A 310 LEU cc_start: 0.9054 (mt) cc_final: 0.8831 (mp) REVERT: A 371 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8246 (p) outliers start: 20 outliers final: 13 residues processed: 72 average time/residue: 0.0498 time to fit residues: 4.8372 Evaluate side-chains 72 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 593 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.148573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.123788 restraints weight = 6609.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.126629 restraints weight = 3561.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128419 restraints weight = 2532.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.129158 restraints weight = 2094.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.129956 restraints weight = 1921.126| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4316 Z= 0.164 Angle : 0.568 9.323 5859 Z= 0.300 Chirality : 0.041 0.150 677 Planarity : 0.005 0.071 715 Dihedral : 7.939 58.086 712 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.56 % Allowed : 22.71 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.38), residues: 535 helix: 1.80 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.30 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 298 TYR 0.012 0.001 TYR A 430 PHE 0.027 0.001 PHE A 229 TRP 0.007 0.001 TRP A 354 HIS 0.003 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4316) covalent geometry : angle 0.56795 ( 5859) hydrogen bonds : bond 0.06773 ( 256) hydrogen bonds : angle 4.12244 ( 762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.169 Fit side-chains REVERT: A 310 LEU cc_start: 0.9091 (mt) cc_final: 0.8865 (mp) REVERT: A 427 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7542 (mt) outliers start: 23 outliers final: 18 residues processed: 79 average time/residue: 0.0504 time to fit residues: 5.4857 Evaluate side-chains 81 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 593 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.151227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126712 restraints weight = 6590.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.129590 restraints weight = 3501.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131475 restraints weight = 2475.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.132223 restraints weight = 2031.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132699 restraints weight = 1856.040| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4316 Z= 0.129 Angle : 0.531 7.384 5859 Z= 0.280 Chirality : 0.039 0.149 677 Planarity : 0.005 0.072 715 Dihedral : 7.495 51.635 712 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.07 % Allowed : 23.43 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.38), residues: 535 helix: 1.81 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -1.24 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 298 TYR 0.018 0.001 TYR A 92 PHE 0.018 0.001 PHE A 229 TRP 0.009 0.001 TRP A 354 HIS 0.002 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 4316) covalent geometry : angle 0.53132 ( 5859) hydrogen bonds : bond 0.06032 ( 256) hydrogen bonds : angle 3.96203 ( 762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.147 Fit side-chains REVERT: A 310 LEU cc_start: 0.9066 (mt) cc_final: 0.8850 (mp) REVERT: A 371 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8368 (p) outliers start: 21 outliers final: 17 residues processed: 77 average time/residue: 0.0489 time to fit residues: 5.2198 Evaluate side-chains 81 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 593 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 23 optimal weight: 0.0470 chunk 48 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.151814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.127192 restraints weight = 6751.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130155 restraints weight = 3556.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132048 restraints weight = 2492.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.133105 restraints weight = 2036.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.133454 restraints weight = 1820.310| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4316 Z= 0.125 Angle : 0.528 6.864 5859 Z= 0.276 Chirality : 0.040 0.135 677 Planarity : 0.005 0.071 715 Dihedral : 7.065 57.345 712 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.80 % Allowed : 22.95 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.38), residues: 535 helix: 1.83 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -1.22 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 298 TYR 0.016 0.001 TYR A 242 PHE 0.019 0.001 PHE A 229 TRP 0.007 0.001 TRP A 354 HIS 0.002 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4316) covalent geometry : angle 0.52799 ( 5859) hydrogen bonds : bond 0.05717 ( 256) hydrogen bonds : angle 3.91617 ( 762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.147 Fit side-chains REVERT: A 346 SER cc_start: 0.7445 (m) cc_final: 0.7044 (p) REVERT: A 371 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8423 (p) outliers start: 24 outliers final: 19 residues processed: 80 average time/residue: 0.0521 time to fit residues: 5.7116 Evaluate side-chains 85 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 593 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 0.0070 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.0570 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.128524 restraints weight = 6679.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.131490 restraints weight = 3511.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133365 restraints weight = 2465.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.134092 restraints weight = 2025.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.135022 restraints weight = 1853.763| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4316 Z= 0.119 Angle : 0.519 6.851 5859 Z= 0.274 Chirality : 0.039 0.138 677 Planarity : 0.005 0.071 715 Dihedral : 6.711 55.689 712 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.07 % Allowed : 24.40 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.38), residues: 535 helix: 1.87 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -1.20 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 298 TYR 0.017 0.001 TYR A 92 PHE 0.017 0.001 PHE A 229 TRP 0.008 0.001 TRP A 354 HIS 0.002 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 4316) covalent geometry : angle 0.51926 ( 5859) hydrogen bonds : bond 0.05440 ( 256) hydrogen bonds : angle 3.85574 ( 762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.147 Fit side-chains REVERT: A 346 SER cc_start: 0.7440 (m) cc_final: 0.7041 (p) REVERT: A 371 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8375 (p) outliers start: 21 outliers final: 18 residues processed: 83 average time/residue: 0.0514 time to fit residues: 5.8987 Evaluate side-chains 86 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 593 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.151471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126891 restraints weight = 6668.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.129845 restraints weight = 3561.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131665 restraints weight = 2512.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132787 restraints weight = 2072.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.133190 restraints weight = 1848.746| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4316 Z= 0.129 Angle : 0.539 6.965 5859 Z= 0.281 Chirality : 0.040 0.141 677 Planarity : 0.005 0.072 715 Dihedral : 6.327 42.518 712 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 5.80 % Allowed : 23.91 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.38), residues: 535 helix: 1.85 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -1.20 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 298 TYR 0.017 0.001 TYR A 242 PHE 0.020 0.001 PHE A 229 TRP 0.005 0.001 TRP A 249 HIS 0.002 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4316) covalent geometry : angle 0.53886 ( 5859) hydrogen bonds : bond 0.05679 ( 256) hydrogen bonds : angle 3.89323 ( 762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.170 Fit side-chains REVERT: A 346 SER cc_start: 0.7373 (m) cc_final: 0.6901 (t) outliers start: 24 outliers final: 18 residues processed: 83 average time/residue: 0.0510 time to fit residues: 5.8347 Evaluate side-chains 84 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 593 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 38 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.152378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.127766 restraints weight = 6734.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.130738 restraints weight = 3545.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.132645 restraints weight = 2489.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133535 restraints weight = 2054.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134331 restraints weight = 1851.018| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4316 Z= 0.125 Angle : 0.544 6.811 5859 Z= 0.281 Chirality : 0.040 0.227 677 Planarity : 0.005 0.072 715 Dihedral : 6.088 40.628 712 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.59 % Allowed : 25.36 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.38), residues: 535 helix: 1.83 (0.29), residues: 351 sheet: None (None), residues: 0 loop : -1.22 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 298 TYR 0.016 0.001 TYR A 92 PHE 0.018 0.001 PHE A 229 TRP 0.007 0.001 TRP A 354 HIS 0.002 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 4316) covalent geometry : angle 0.54422 ( 5859) hydrogen bonds : bond 0.05549 ( 256) hydrogen bonds : angle 3.89415 ( 762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.148 Fit side-chains REVERT: A 346 SER cc_start: 0.7486 (m) cc_final: 0.7055 (t) REVERT: A 601 MET cc_start: 0.7769 (tpp) cc_final: 0.7108 (mmt) outliers start: 19 outliers final: 17 residues processed: 78 average time/residue: 0.0499 time to fit residues: 5.3885 Evaluate side-chains 83 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 593 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 18 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.150323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.125807 restraints weight = 6625.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128678 restraints weight = 3565.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130474 restraints weight = 2531.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131355 restraints weight = 2097.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131491 restraints weight = 1905.367| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4316 Z= 0.141 Angle : 0.567 6.956 5859 Z= 0.292 Chirality : 0.042 0.220 677 Planarity : 0.005 0.072 715 Dihedral : 5.955 37.694 712 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.35 % Allowed : 25.36 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.38), residues: 535 helix: 1.73 (0.29), residues: 351 sheet: None (None), residues: 0 loop : -1.26 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 298 TYR 0.018 0.001 TYR A 242 PHE 0.022 0.001 PHE A 229 TRP 0.004 0.001 TRP A 354 HIS 0.002 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4316) covalent geometry : angle 0.56728 ( 5859) hydrogen bonds : bond 0.05968 ( 256) hydrogen bonds : angle 4.01068 ( 762) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.154 Fit side-chains REVERT: A 346 SER cc_start: 0.7527 (m) cc_final: 0.7069 (t) REVERT: A 601 MET cc_start: 0.7857 (tpp) cc_final: 0.7162 (mmt) outliers start: 18 outliers final: 17 residues processed: 79 average time/residue: 0.0499 time to fit residues: 5.4610 Evaluate side-chains 83 residues out of total 447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 593 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.151097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126480 restraints weight = 6676.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129429 restraints weight = 3566.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.131286 restraints weight = 2529.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132174 restraints weight = 2084.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132767 restraints weight = 1891.459| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4316 Z= 0.132 Angle : 0.564 8.135 5859 Z= 0.292 Chirality : 0.041 0.214 677 Planarity : 0.005 0.072 715 Dihedral : 5.827 34.852 712 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.11 % Allowed : 25.85 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.38), residues: 535 helix: 1.74 (0.29), residues: 351 sheet: None (None), residues: 0 loop : -1.25 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 298 TYR 0.017 0.001 TYR A 92 PHE 0.019 0.001 PHE A 229 TRP 0.007 0.001 TRP A 354 HIS 0.002 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4316) covalent geometry : angle 0.56396 ( 5859) hydrogen bonds : bond 0.05709 ( 256) hydrogen bonds : angle 4.00649 ( 762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 823.49 seconds wall clock time: 14 minutes 50.68 seconds (890.68 seconds total)