Starting phenix.real_space_refine on Wed Jul 1 22:54:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9unx_64368/07_2026/9unx_64368.cif Found real_map, /net/cci-nas-00/data/ceres_data/9unx_64368/07_2026/9unx_64368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9unx_64368/07_2026/9unx_64368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9unx_64368/07_2026/9unx_64368.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9unx_64368/07_2026/9unx_64368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9unx_64368/07_2026/9unx_64368.map" } resolution = 3.45 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= 0.000 sd= 0.026 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 29 5.16 5 C 2375 2.51 5 N 620 2.21 5 O 622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3647 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3613 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain breaks: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Ad-hoc single atom residues: {' BR': 1} Unusual residues: {'OLM': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 1.01, per 1000 atoms: 0.28 Number of scatterers: 3647 At special positions: 0 Unit cell: (96.5016, 59.3856, 71.7576, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 29 16.00 O 622 8.00 N 620 7.00 C 2375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.03 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: 0.32 Conformation dependent library (CDL) restraints added in 133.5 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 862 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 81.4% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 14 through 26 Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.986A pdb=" N ALA A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 131 through 159 removed outlier: 4.026A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 181 removed outlier: 3.727A pdb=" N VAL A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 213 removed outlier: 3.536A pdb=" N TYR A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.566A pdb=" N GLY A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 removed outlier: 3.589A pdb=" N LEU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.919A pdb=" N ALA A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 297 through 304 removed outlier: 3.555A pdb=" N GLY A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 332 through 358 removed outlier: 3.921A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 377 through 392 Processing helix chain 'A' and resid 393 through 415 removed outlier: 3.878A pdb=" N GLY A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 448 removed outlier: 3.750A pdb=" N GLY A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 484 through 491 Processing helix chain 'A' and resid 492 through 504 removed outlier: 4.164A pdb=" N ALA A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 243 hydrogen bonds defined for protein. 720 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: 0.49 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1122 1.34 - 1.45: 523 1.45 - 1.57: 2043 1.57 - 1.69: 2 1.69 - 1.81: 45 Bond restraints: 3735 Sorted by residual: bond pdb=" C15 OLM A 602 " pdb=" C18 OLM A 602 " ideal model delta sigma weight residual 1.491 1.583 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C5 OLM A 602 " pdb=" C8 OLM A 602 " ideal model delta sigma weight residual 1.479 1.567 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C13 OLM A 602 " pdb=" C14 OLM A 602 " ideal model delta sigma weight residual 1.463 1.509 -0.046 2.00e-02 2.50e+03 5.29e+00 bond pdb=" C ILE A 269 " pdb=" N GLU A 270 " ideal model delta sigma weight residual 1.330 1.300 0.029 1.31e-02 5.83e+03 5.05e+00 bond pdb=" C16 OLM A 602 " pdb=" N6 OLM A 602 " ideal model delta sigma weight residual 1.368 1.325 0.043 2.00e-02 2.50e+03 4.69e+00 ... (remaining 3730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 4981 1.46 - 2.92: 68 2.92 - 4.38: 22 4.38 - 5.84: 12 5.84 - 7.30: 1 Bond angle restraints: 5084 Sorted by residual: angle pdb=" CA PRO A 333 " pdb=" N PRO A 333 " pdb=" CD PRO A 333 " ideal model delta sigma weight residual 112.00 107.84 4.16 1.40e+00 5.10e-01 8.82e+00 angle pdb=" O1 OLM A 602 " pdb=" C21 OLM A 602 " pdb=" O2 OLM A 602 " ideal model delta sigma weight residual 127.27 119.97 7.30 3.00e+00 1.11e-01 5.92e+00 angle pdb=" CA MET A 452 " pdb=" CB MET A 452 " pdb=" CG MET A 452 " ideal model delta sigma weight residual 114.10 118.40 -4.30 2.00e+00 2.50e-01 4.63e+00 angle pdb=" N PRO A 333 " pdb=" CD PRO A 333 " pdb=" CG PRO A 333 " ideal model delta sigma weight residual 103.20 100.27 2.93 1.50e+00 4.44e-01 3.83e+00 angle pdb=" C16 OLM A 602 " pdb=" C17 OLM A 602 " pdb=" C21 OLM A 602 " ideal model delta sigma weight residual 132.53 127.13 5.40 3.00e+00 1.11e-01 3.24e+00 ... (remaining 5079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.14: 2055 28.14 - 56.29: 126 56.29 - 84.43: 15 84.43 - 112.58: 0 112.58 - 140.72: 1 Dihedral angle restraints: 2197 sinusoidal: 856 harmonic: 1341 Sorted by residual: dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual -86.00 -166.36 80.36 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" C3 OLM A 602 " pdb=" C1 OLM A 602 " pdb=" C2 OLM A 602 " pdb=" N1 OLM A 602 " ideal model delta sinusoidal sigma weight residual -125.43 15.29 -140.72 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CG ARG A 454 " pdb=" CD ARG A 454 " pdb=" NE ARG A 454 " pdb=" CZ ARG A 454 " ideal model delta sinusoidal sigma weight residual 90.00 134.97 -44.97 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 2194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 385 0.026 - 0.052: 131 0.052 - 0.078: 45 0.078 - 0.104: 20 0.104 - 0.130: 6 Chirality restraints: 587 Sorted by residual: chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE A 415 " pdb=" N ILE A 415 " pdb=" C ILE A 415 " pdb=" CB ILE A 415 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA VAL A 365 " pdb=" N VAL A 365 " pdb=" C VAL A 365 " pdb=" CB VAL A 365 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 584 not shown) Planarity restraints: 633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 332 " 0.057 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO A 333 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 67 " 0.032 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 68 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 116 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO A 117 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.024 5.00e-02 4.00e+02 ... (remaining 630 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 892 2.79 - 3.32: 3525 3.32 - 3.84: 6028 3.84 - 4.37: 6950 4.37 - 4.90: 12102 Nonbonded interactions: 29497 Sorted by model distance: nonbonded pdb=" OG SER A 175 " pdb=" O PHE A 191 " model vdw 2.262 3.040 nonbonded pdb=" O ARG A 273 " pdb=" OG SER A 276 " model vdw 2.298 3.040 nonbonded pdb=" O SER A 278 " pdb=" OG SER A 278 " model vdw 2.368 3.040 nonbonded pdb=" OE2 GLU A 506 " pdb=" N LEU A 508 " model vdw 2.417 3.120 nonbonded pdb=" O GLY A 446 " pdb=" NE ARG A 454 " model vdw 2.432 3.120 ... (remaining 29492 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.170 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 : 0.004 0.092 3737 Z= 0.195 Angle : 0.528 7.300 5088 Z= 0.251 Chirality : 0.035 0.130 587 Planarity : 0.005 0.085 633 Dihedral : 16.726 140.721 1329 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 23.71 % Favored : 76.29 % 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: 0.04 (0.39), residues: 459 helix: 0.17 (0.28), residues: 341 sheet: 0.23 (1.90), residues: 10 loop : 0.02 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 80 TYR 0.006 0.001 TYR A 353 PHE 0.013 0.001 PHE A 262 TRP 0.006 0.001 TRP A 274 HIS 0.002 0.000 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 ( 3735) covalent geometry : angle 0.52783 / 0.25 ( 5084) SS BOND : bond 0.00325 / 0.16 ( 2) SS BOND : angle 0.34475 / 0.22 ( 4) hydrogen bonds : bond 0.26387 / 17.04 ( 243) hydrogen bonds : angle 8.15495 / 5.73 ( 720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.141 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0695 time to fit residues: 5.6078 Evaluate side-chains 59 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.148380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122267 restraints weight = 4335.768| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.98 r_work: 0.3251 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3737 Z= 0.157 Angle : 0.575 5.721 5088 Z= 0.291 Chirality : 0.040 0.133 587 Planarity : 0.005 0.057 633 Dihedral : 8.759 136.800 520 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.87 % Allowed : 20.62 % Favored : 75.52 % 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: 1.00 (0.40), residues: 459 helix: 0.99 (0.28), residues: 352 sheet: -0.10 (1.85), residues: 10 loop : -0.15 (0.63), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 454 TYR 0.014 0.001 TYR A 264 PHE 0.017 0.001 PHE A 258 TRP 0.010 0.001 TRP A 247 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 3735) covalent geometry : angle 0.57453 / 0.29 ( 5084) SS BOND : bond 0.00763 / 0.37 ( 2) SS BOND : angle 0.64814 / 0.39 ( 4) hydrogen bonds : bond 0.05362 / 3.48 ( 243) hydrogen bonds : angle 4.89329 / 3.44 ( 720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.128 Fit side-chains REVERT: A 81 PHE cc_start: 0.8002 (m-80) cc_final: 0.7677 (m-80) REVERT: A 236 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7279 (tt) REVERT: A 359 ASP cc_start: 0.8349 (t0) cc_final: 0.7975 (m-30) REVERT: A 454 ARG cc_start: 0.7636 (ttm170) cc_final: 0.7266 (ttm170) REVERT: A 506 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7802 (tp30) outliers start: 15 outliers final: 10 residues processed: 79 average time/residue: 0.0540 time to fit residues: 5.5840 Evaluate side-chains 73 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121493 restraints weight = 4313.459| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.01 r_work: 0.3231 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3737 Z= 0.151 Angle : 0.588 8.094 5088 Z= 0.282 Chirality : 0.039 0.131 587 Planarity : 0.004 0.052 633 Dihedral : 8.252 135.821 520 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.90 % Allowed : 21.65 % Favored : 73.45 % 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: 1.32 (0.40), residues: 459 helix: 1.26 (0.28), residues: 347 sheet: -0.05 (1.87), residues: 10 loop : -0.12 (0.61), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 454 TYR 0.014 0.001 TYR A 264 PHE 0.013 0.001 PHE A 258 TRP 0.009 0.001 TRP A 247 HIS 0.004 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 3735) covalent geometry : angle 0.58800 / 0.28 ( 5084) SS BOND : bond 0.00798 / 0.38 ( 2) SS BOND : angle 0.79644 / 0.44 ( 4) hydrogen bonds : bond 0.04587 / 2.93 ( 243) hydrogen bonds : angle 4.50179 / 3.17 ( 720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.127 Fit side-chains REVERT: A 81 PHE cc_start: 0.8009 (m-80) cc_final: 0.7662 (m-80) REVERT: A 338 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6971 (tt) REVERT: A 359 ASP cc_start: 0.8398 (t0) cc_final: 0.8150 (t0) REVERT: A 448 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8590 (tp) REVERT: A 454 ARG cc_start: 0.7641 (ttm170) cc_final: 0.7309 (ttm170) outliers start: 19 outliers final: 13 residues processed: 76 average time/residue: 0.0629 time to fit residues: 6.1431 Evaluate side-chains 74 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.153265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.127633 restraints weight = 4164.401| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.81 r_work: 0.3305 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3737 Z= 0.112 Angle : 0.572 13.008 5088 Z= 0.266 Chirality : 0.037 0.127 587 Planarity : 0.004 0.043 633 Dihedral : 7.794 133.353 520 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.64 % Allowed : 23.45 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.72 (0.40), residues: 459 helix: 1.57 (0.29), residues: 347 sheet: 0.08 (1.85), residues: 10 loop : -0.05 (0.60), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.010 0.001 TYR A 264 PHE 0.012 0.001 PHE A 258 TRP 0.007 0.001 TRP A 247 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 3735) covalent geometry : angle 0.57221 / 0.27 ( 5084) SS BOND : bond 0.00554 / 0.26 ( 2) SS BOND : angle 0.65929 / 0.37 ( 4) hydrogen bonds : bond 0.03772 / 2.40 ( 243) hydrogen bonds : angle 4.21956 / 2.96 ( 720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.129 Fit side-chains REVERT: A 140 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7787 (mt) REVERT: A 338 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6754 (tt) REVERT: A 359 ASP cc_start: 0.8382 (t0) cc_final: 0.8112 (t0) REVERT: A 448 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8552 (tp) outliers start: 18 outliers final: 11 residues processed: 70 average time/residue: 0.0491 time to fit residues: 4.5139 Evaluate side-chains 67 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 31 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.154047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.128591 restraints weight = 4173.436| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.80 r_work: 0.3314 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3737 Z= 0.110 Angle : 0.556 12.737 5088 Z= 0.258 Chirality : 0.037 0.128 587 Planarity : 0.004 0.038 633 Dihedral : 7.521 132.867 520 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.67 % Allowed : 21.91 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.91 (0.40), residues: 459 helix: 1.72 (0.29), residues: 350 sheet: 0.08 (1.84), residues: 10 loop : -0.09 (0.60), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.010 0.001 TYR A 264 PHE 0.015 0.001 PHE A 152 TRP 0.007 0.001 TRP A 247 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 3735) covalent geometry : angle 0.55623 / 0.26 ( 5084) SS BOND : bond 0.00522 / 0.25 ( 2) SS BOND : angle 0.62181 / 0.36 ( 4) hydrogen bonds : bond 0.03589 / 2.30 ( 243) hydrogen bonds : angle 4.09816 / 2.88 ( 720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.153 Fit side-chains REVERT: A 81 PHE cc_start: 0.8194 (m-80) cc_final: 0.7935 (m-80) REVERT: A 140 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7755 (mt) REVERT: A 236 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7396 (tt) REVERT: A 338 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6675 (tt) REVERT: A 359 ASP cc_start: 0.8382 (t0) cc_final: 0.7940 (m-30) REVERT: A 448 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8461 (tp) outliers start: 22 outliers final: 14 residues processed: 68 average time/residue: 0.0344 time to fit residues: 3.1945 Evaluate side-chains 65 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.0770 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.152470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.127062 restraints weight = 4201.593| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.80 r_work: 0.3297 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3737 Z= 0.123 Angle : 0.547 11.215 5088 Z= 0.260 Chirality : 0.038 0.129 587 Planarity : 0.004 0.036 633 Dihedral : 7.445 132.593 520 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 7.22 % Allowed : 22.16 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.95 (0.40), residues: 459 helix: 1.75 (0.29), residues: 348 sheet: 0.00 (1.81), residues: 10 loop : -0.04 (0.60), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.013 0.001 TYR A 264 PHE 0.021 0.001 PHE A 347 TRP 0.007 0.001 TRP A 247 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 3735) covalent geometry : angle 0.54677 / 0.26 ( 5084) SS BOND : bond 0.00646 / 0.31 ( 2) SS BOND : angle 0.69505 / 0.38 ( 4) hydrogen bonds : bond 0.03656 / 2.33 ( 243) hydrogen bonds : angle 4.08646 / 2.88 ( 720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.131 Fit side-chains REVERT: A 81 PHE cc_start: 0.8173 (m-80) cc_final: 0.7906 (m-80) REVERT: A 131 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7743 (mtm-85) REVERT: A 140 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7780 (mt) REVERT: A 236 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7391 (tt) REVERT: A 338 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6742 (tt) REVERT: A 359 ASP cc_start: 0.8488 (t0) cc_final: 0.8024 (m-30) REVERT: A 444 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.7402 (t80) REVERT: A 448 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8369 (tp) outliers start: 28 outliers final: 18 residues processed: 77 average time/residue: 0.0463 time to fit residues: 4.6089 Evaluate side-chains 78 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.151794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126321 restraints weight = 4304.783| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.82 r_work: 0.3290 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3737 Z= 0.129 Angle : 0.579 13.980 5088 Z= 0.271 Chirality : 0.039 0.128 587 Planarity : 0.004 0.034 633 Dihedral : 7.422 131.877 520 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 7.22 % Allowed : 22.94 % Favored : 69.85 % 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: 1.94 (0.40), residues: 459 helix: 1.74 (0.29), residues: 348 sheet: 0.03 (1.82), residues: 10 loop : -0.05 (0.59), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 298 TYR 0.013 0.001 TYR A 264 PHE 0.010 0.001 PHE A 152 TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 3735) covalent geometry : angle 0.57842 / 0.27 ( 5084) SS BOND : bond 0.00661 / 0.32 ( 2) SS BOND : angle 0.69272 / 0.38 ( 4) hydrogen bonds : bond 0.03715 / 2.38 ( 243) hydrogen bonds : angle 4.10781 / 2.90 ( 720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.127 Fit side-chains REVERT: A 81 PHE cc_start: 0.8192 (m-80) cc_final: 0.7921 (m-80) REVERT: A 131 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7743 (mtm-85) REVERT: A 140 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7802 (mt) REVERT: A 236 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7383 (tt) REVERT: A 338 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6798 (tt) REVERT: A 359 ASP cc_start: 0.8530 (t0) cc_final: 0.8069 (m-30) REVERT: A 444 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7433 (t80) REVERT: A 448 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8334 (tp) outliers start: 28 outliers final: 19 residues processed: 82 average time/residue: 0.0543 time to fit residues: 5.7856 Evaluate side-chains 81 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.151038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.125802 restraints weight = 4175.915| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.77 r_work: 0.3280 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3737 Z= 0.140 Angle : 0.604 14.729 5088 Z= 0.282 Chirality : 0.039 0.133 587 Planarity : 0.004 0.033 633 Dihedral : 7.420 131.431 520 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 7.22 % Allowed : 23.71 % Favored : 69.07 % 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: 1.92 (0.40), residues: 459 helix: 1.71 (0.29), residues: 347 sheet: -0.03 (1.80), residues: 10 loop : 0.03 (0.59), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.014 0.001 TYR A 264 PHE 0.025 0.002 PHE A 347 TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 3735) covalent geometry : angle 0.60376 / 0.28 ( 5084) SS BOND : bond 0.00728 / 0.35 ( 2) SS BOND : angle 0.72033 / 0.39 ( 4) hydrogen bonds : bond 0.03806 / 2.45 ( 243) hydrogen bonds : angle 4.15095 / 2.94 ( 720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 0.088 Fit side-chains REVERT: A 81 PHE cc_start: 0.8168 (m-80) cc_final: 0.7884 (m-80) REVERT: A 140 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7794 (mt) REVERT: A 236 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7384 (tt) REVERT: A 338 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6639 (tt) REVERT: A 342 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7372 (mp) REVERT: A 444 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7400 (t80) outliers start: 28 outliers final: 21 residues processed: 82 average time/residue: 0.0480 time to fit residues: 5.2234 Evaluate side-chains 80 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.152535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.127080 restraints weight = 4156.351| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.81 r_work: 0.3301 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3737 Z= 0.121 Angle : 0.595 15.662 5088 Z= 0.278 Chirality : 0.038 0.129 587 Planarity : 0.004 0.032 633 Dihedral : 7.387 130.584 520 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 6.96 % Allowed : 23.71 % Favored : 69.33 % 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: 1.97 (0.40), residues: 459 helix: 1.73 (0.29), residues: 351 sheet: 0.00 (1.82), residues: 10 loop : 0.06 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 336 TYR 0.011 0.001 TYR A 264 PHE 0.010 0.001 PHE A 258 TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 3735) covalent geometry : angle 0.59459 / 0.28 ( 5084) SS BOND : bond 0.00604 / 0.29 ( 2) SS BOND : angle 0.64401 / 0.37 ( 4) hydrogen bonds : bond 0.03630 / 2.35 ( 243) hydrogen bonds : angle 4.09434 / 2.90 ( 720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 0.170 Fit side-chains REVERT: A 9 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7357 (tp40) REVERT: A 140 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7806 (mt) REVERT: A 338 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6628 (tt) REVERT: A 342 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7379 (mp) REVERT: A 359 ASP cc_start: 0.8378 (t0) cc_final: 0.7937 (m-30) REVERT: A 444 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7391 (t80) outliers start: 27 outliers final: 20 residues processed: 77 average time/residue: 0.0437 time to fit residues: 4.4482 Evaluate side-chains 77 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.152084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126561 restraints weight = 4246.949| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.84 r_work: 0.3295 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3737 Z= 0.127 Angle : 0.614 15.711 5088 Z= 0.287 Chirality : 0.039 0.130 587 Planarity : 0.004 0.032 633 Dihedral : 7.385 130.644 520 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 6.96 % Allowed : 23.97 % Favored : 69.07 % 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: 1.96 (0.40), residues: 459 helix: 1.71 (0.29), residues: 351 sheet: -0.04 (1.80), residues: 10 loop : 0.13 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.012 0.001 TYR A 264 PHE 0.028 0.002 PHE A 347 TRP 0.008 0.001 TRP A 247 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 3735) covalent geometry : angle 0.61357 / 0.29 ( 5084) SS BOND : bond 0.00601 / 0.29 ( 2) SS BOND : angle 0.60516 / 0.35 ( 4) hydrogen bonds : bond 0.03668 / 2.39 ( 243) hydrogen bonds : angle 4.09154 / 2.90 ( 720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 54 time to evaluate : 0.088 Fit side-chains REVERT: A 9 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7378 (tp40) REVERT: A 81 PHE cc_start: 0.8140 (m-80) cc_final: 0.7881 (m-80) REVERT: A 140 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7796 (mt) REVERT: A 236 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7386 (tt) REVERT: A 338 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6727 (tt) REVERT: A 342 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7375 (mp) REVERT: A 359 ASP cc_start: 0.8419 (t0) cc_final: 0.7996 (m-30) REVERT: A 444 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7388 (t80) outliers start: 27 outliers final: 21 residues processed: 77 average time/residue: 0.0368 time to fit residues: 3.7575 Evaluate side-chains 79 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.152607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.126914 restraints weight = 4143.612| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.79 r_work: 0.3303 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3737 Z= 0.124 Angle : 0.611 15.441 5088 Z= 0.286 Chirality : 0.039 0.129 587 Planarity : 0.004 0.032 633 Dihedral : 7.397 130.463 520 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 7.22 % Allowed : 23.71 % Favored : 69.07 % 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: 1.96 (0.40), residues: 459 helix: 1.70 (0.29), residues: 351 sheet: -0.02 (1.81), residues: 10 loop : 0.17 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.011 0.001 TYR A 264 PHE 0.010 0.001 PHE A 258 TRP 0.008 0.001 TRP A 247 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 3735) covalent geometry : angle 0.61051 / 0.29 ( 5084) SS BOND : bond 0.00591 / 0.28 ( 2) SS BOND : angle 0.60349 / 0.35 ( 4) hydrogen bonds : bond 0.03671 / 2.40 ( 243) hydrogen bonds : angle 4.08836 / 2.90 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 972.11 seconds wall clock time: 17 minutes 21.18 seconds (1041.18 seconds total)