Starting phenix.real_space_refine on Wed Jul 1 22:37:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ctj_26992/07_2026/8ctj_26992.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ctj_26992/07_2026/8ctj_26992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ctj_26992/07_2026/8ctj_26992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ctj_26992/07_2026/8ctj_26992.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ctj_26992/07_2026/8ctj_26992.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ctj_26992/07_2026/8ctj_26992.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ctj_26992/07_2026/8ctj_26992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ctj_26992/07_2026/8ctj_26992.cif" } resolution = 4.74 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= 0.005 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 P 1 5.49 5 S 18 5.16 5 C 2202 2.51 5 N 529 2.21 5 O 562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 3312 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3286 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Time building chain proxies: 0.75, per 1000 atoms: 0.23 Number of scatterers: 3312 At special positions: 0 Unit cell: (55.75, 57.98, 105.925, 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) S 18 16.00 P 1 15.00 O 562 8.00 N 529 7.00 C 2202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 128 " distance=2.04 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 431 " 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: 0.19 Conformation dependent library (CDL) restraints added in 107.7 milliseconds 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 3 sheets defined 59.6% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.776A pdb=" N TYR A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 110 removed outlier: 4.056A pdb=" N GLU A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 removed outlier: 3.745A pdb=" N LEU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 132 " --> pdb=" O CYS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 251 removed outlier: 3.647A pdb=" N MET A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 228 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N CYS A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR A 251 " --> pdb=" O TRP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 285 removed outlier: 3.586A pdb=" N PHE A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 317 removed outlier: 3.642A pdb=" N LEU A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 353 removed outlier: 4.554A pdb=" N MET A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 393 removed outlier: 4.074A pdb=" N PHE A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Proline residue: A 366 - end of helix Processing helix chain 'A' and resid 394 through 428 removed outlier: 3.747A pdb=" N ARG A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 465 through 471 removed outlier: 4.007A pdb=" N PHE A 471 " --> pdb=" O GLN A 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 59 228 hydrogen bonds defined for protein. 663 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: 0.28 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: 977 1.34 - 1.47: 929 1.47 - 1.60: 1461 1.60 - 1.73: 1 1.73 - 1.86: 30 Bond restraints: 3398 Sorted by residual: bond pdb=" O4P PEE A 601 " pdb=" P PEE A 601 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" C1 PEE A 601 " pdb=" C2 PEE A 601 " ideal model delta sigma weight residual 1.519 1.555 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" CA ASP A 75 " pdb=" CB ASP A 75 " ideal model delta sigma weight residual 1.531 1.577 -0.047 3.12e-02 1.03e+03 2.25e+00 bond pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " ideal model delta sigma weight residual 1.808 1.855 -0.047 3.30e-02 9.18e+02 2.05e+00 bond pdb=" C2 PEE A 601 " pdb=" C3 PEE A 601 " ideal model delta sigma weight residual 1.512 1.540 -0.028 2.00e-02 2.50e+03 2.03e+00 ... (remaining 3393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 4511 2.78 - 5.57: 71 5.57 - 8.35: 20 8.35 - 11.14: 0 11.14 - 13.92: 1 Bond angle restraints: 4603 Sorted by residual: angle pdb=" O1P PEE A 601 " pdb=" P PEE A 601 " pdb=" O2P PEE A 601 " ideal model delta sigma weight residual 119.43 133.35 -13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CA LYS A 213 " pdb=" CB LYS A 213 " pdb=" CG LYS A 213 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.49e+01 angle pdb=" N GLN A 135 " pdb=" CA GLN A 135 " pdb=" C GLN A 135 " ideal model delta sigma weight residual 110.44 106.16 4.28 1.20e+00 6.94e-01 1.27e+01 angle pdb=" CA TRP A 252 " pdb=" CB TRP A 252 " pdb=" CG TRP A 252 " ideal model delta sigma weight residual 113.60 120.05 -6.45 1.90e+00 2.77e-01 1.15e+01 angle pdb=" CA MET A 231 " pdb=" CB MET A 231 " pdb=" CG MET A 231 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 ... (remaining 4598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 1800 17.14 - 34.28: 140 34.28 - 51.42: 25 51.42 - 68.56: 7 68.56 - 85.70: 4 Dihedral angle restraints: 1976 sinusoidal: 799 harmonic: 1177 Sorted by residual: dihedral pdb=" CB CYS A 89 " pdb=" SG CYS A 89 " pdb=" SG CYS A 431 " pdb=" CB CYS A 431 " ideal model delta sinusoidal sigma weight residual 93.00 144.73 -51.73 1 1.00e+01 1.00e-02 3.65e+01 dihedral pdb=" CA ASN A 394 " pdb=" C ASN A 394 " pdb=" N ILE A 395 " pdb=" CA ILE A 395 " ideal model delta harmonic sigma weight residual -180.00 -161.55 -18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA PHE A 230 " pdb=" C PHE A 230 " pdb=" N MET A 231 " pdb=" CA MET A 231 " ideal model delta harmonic sigma weight residual 180.00 162.98 17.02 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 1973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 459 0.077 - 0.155: 54 0.155 - 0.232: 6 0.232 - 0.309: 0 0.309 - 0.387: 1 Chirality restraints: 520 Sorted by residual: chirality pdb=" C2 PEE A 601 " pdb=" C1 PEE A 601 " pdb=" C3 PEE A 601 " pdb=" O2 PEE A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.71 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB ILE A 44 " pdb=" CA ILE A 44 " pdb=" CG1 ILE A 44 " pdb=" CG2 ILE A 44 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB THR A 405 " pdb=" CA THR A 405 " pdb=" OG1 THR A 405 " pdb=" CG2 THR A 405 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 517 not shown) Planarity restraints: 551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 371 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" CG ASP A 371 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP A 371 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 371 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 135 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C GLN A 135 " -0.038 2.00e-02 2.50e+03 pdb=" O GLN A 135 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 136 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 404 " -0.010 2.00e-02 2.50e+03 1.54e-02 4.17e+00 pdb=" CG PHE A 404 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 404 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 404 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 404 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 404 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 404 " 0.001 2.00e-02 2.50e+03 ... (remaining 548 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 536 2.77 - 3.30: 3273 3.30 - 3.83: 5397 3.83 - 4.37: 5945 4.37 - 4.90: 10260 Nonbonded interactions: 25411 Sorted by model distance: nonbonded pdb=" O TYR A 340 " pdb=" OG SER A 344 " model vdw 2.233 3.040 nonbonded pdb=" OG SER A 77 " pdb=" O SER A 191 " model vdw 2.233 3.040 nonbonded pdb=" O ILE A 419 " pdb=" OG1 THR A 423 " model vdw 2.276 3.040 nonbonded pdb=" O ASN A 200 " pdb=" OG SER A 203 " model vdw 2.312 3.040 nonbonded pdb=" O SER A 399 " pdb=" ND1 HIS A 403 " model vdw 2.381 3.120 ... (remaining 25406 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.340 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4792 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 : 0.005 0.123 3400 Z= 0.229 Angle : 0.922 13.923 4607 Z= 0.489 Chirality : 0.051 0.387 520 Planarity : 0.006 0.052 551 Dihedral : 13.466 85.696 1208 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -0.72 (0.41), residues: 395 helix: 0.26 (0.32), residues: 229 sheet: -1.55 (0.73), residues: 47 loop : -1.24 (0.56), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 112 TYR 0.018 0.003 TYR A 277 PHE 0.035 0.003 PHE A 379 TRP 0.018 0.002 TRP A 244 HIS 0.001 0.000 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.23 ( 3398) covalent geometry : angle 0.91738 / 0.49 ( 4603) SS BOND : bond 0.00366 / 0.19 ( 2) SS BOND : angle 3.23547 / 1.71 ( 4) hydrogen bonds : bond 0.08706 / 5.95 ( 210) hydrogen bonds : angle 5.67420 / 3.88 ( 663) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.1994 (mtt) cc_final: 0.1692 (mtt) REVERT: A 227 MET cc_start: 0.8191 (tmm) cc_final: 0.7912 (tmm) REVERT: A 270 MET cc_start: 0.4612 (mmt) cc_final: 0.3934 (mmt) REVERT: A 386 MET cc_start: 0.8365 (tpp) cc_final: 0.7974 (tpp) REVERT: A 438 LEU cc_start: 0.6769 (mp) cc_final: 0.6373 (tp) REVERT: A 440 VAL cc_start: 0.9073 (t) cc_final: 0.8751 (p) REVERT: A 453 LEU cc_start: 0.8336 (mt) cc_final: 0.8133 (mt) REVERT: A 457 MET cc_start: 0.5495 (mtm) cc_final: 0.4813 (ptp) REVERT: A 467 GLN cc_start: 0.8176 (tt0) cc_final: 0.7944 (tt0) REVERT: A 468 ARG cc_start: 0.8817 (mtm180) cc_final: 0.7808 (mmm160) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0653 time to fit residues: 8.4897 Evaluate side-chains 86 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0020 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN A 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.204218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.175650 restraints weight = 5721.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.181944 restraints weight = 3733.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.186787 restraints weight = 2570.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.190415 restraints weight = 1849.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.193245 restraints weight = 1380.815| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5109 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3400 Z= 0.144 Angle : 0.640 9.217 4607 Z= 0.333 Chirality : 0.043 0.176 520 Planarity : 0.005 0.043 551 Dihedral : 7.201 81.948 447 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: 0.26 (0.42), residues: 395 helix: 1.15 (0.33), residues: 230 sheet: -1.32 (0.73), residues: 47 loop : -1.03 (0.58), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 393 TYR 0.011 0.002 TYR A 340 PHE 0.019 0.002 PHE A 276 TRP 0.011 0.001 TRP A 252 HIS 0.005 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 3398) covalent geometry : angle 0.63837 / 0.33 ( 4603) SS BOND : bond 0.00201 / 0.10 ( 2) SS BOND : angle 1.56066 / 0.87 ( 4) hydrogen bonds : bond 0.03784 / 2.46 ( 210) hydrogen bonds : angle 4.64342 / 3.14 ( 663) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8198 (mt) cc_final: 0.7872 (mp) REVERT: A 91 ASN cc_start: 0.6915 (m-40) cc_final: 0.6255 (p0) REVERT: A 227 MET cc_start: 0.8363 (tmm) cc_final: 0.7890 (tmm) REVERT: A 386 MET cc_start: 0.8274 (tpp) cc_final: 0.7883 (tpp) REVERT: A 387 LYS cc_start: 0.8978 (tptt) cc_final: 0.8561 (ttmt) REVERT: A 438 LEU cc_start: 0.7329 (mp) cc_final: 0.6825 (tp) REVERT: A 451 MET cc_start: 0.6696 (mtt) cc_final: 0.6485 (mtp) REVERT: A 453 LEU cc_start: 0.8500 (mt) cc_final: 0.8185 (mt) REVERT: A 457 MET cc_start: 0.6092 (mtm) cc_final: 0.5495 (ptp) REVERT: A 467 GLN cc_start: 0.8155 (tt0) cc_final: 0.7931 (tt0) REVERT: A 468 ARG cc_start: 0.8835 (mtm180) cc_final: 0.7584 (mmm160) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0579 time to fit residues: 7.1165 Evaluate side-chains 86 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 17 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 GLN A 135 GLN A 187 HIS A 356 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.207610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.181147 restraints weight = 6087.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.187454 restraints weight = 3910.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.192074 restraints weight = 2667.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.195337 restraints weight = 1900.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.197910 restraints weight = 1412.881| |-----------------------------------------------------------------------------| r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5209 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3400 Z= 0.129 Angle : 0.594 9.858 4607 Z= 0.304 Chirality : 0.041 0.136 520 Planarity : 0.004 0.036 551 Dihedral : 6.953 78.178 447 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % 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: 0.63 (0.43), residues: 395 helix: 1.42 (0.34), residues: 225 sheet: -0.83 (0.70), residues: 54 loop : -0.83 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 393 TYR 0.017 0.002 TYR A 118 PHE 0.020 0.002 PHE A 404 TRP 0.017 0.001 TRP A 177 HIS 0.006 0.001 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 3398) covalent geometry : angle 0.59039 / 0.30 ( 4603) SS BOND : bond 0.00232 / 0.12 ( 2) SS BOND : angle 2.22178 / 1.18 ( 4) hydrogen bonds : bond 0.03663 / 2.38 ( 210) hydrogen bonds : angle 4.52717 / 3.10 ( 663) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8125 (mt) cc_final: 0.7734 (mt) REVERT: A 91 ASN cc_start: 0.7562 (m-40) cc_final: 0.6862 (p0) REVERT: A 97 LYS cc_start: 0.8596 (tmtt) cc_final: 0.8334 (tptp) REVERT: A 142 MET cc_start: 0.3463 (mpp) cc_final: 0.1653 (mtt) REVERT: A 227 MET cc_start: 0.8447 (tmm) cc_final: 0.8008 (tmm) REVERT: A 273 LYS cc_start: 0.7553 (mtpp) cc_final: 0.6959 (ttmm) REVERT: A 298 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7018 (tp30) REVERT: A 386 MET cc_start: 0.8336 (tpp) cc_final: 0.8014 (tpp) REVERT: A 387 LYS cc_start: 0.8928 (tptt) cc_final: 0.8595 (tttp) REVERT: A 438 LEU cc_start: 0.7833 (mp) cc_final: 0.7216 (tp) REVERT: A 453 LEU cc_start: 0.8300 (mt) cc_final: 0.7922 (mt) REVERT: A 457 MET cc_start: 0.5876 (mtm) cc_final: 0.5363 (ptp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0527 time to fit residues: 6.4187 Evaluate side-chains 80 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 GLN A 143 HIS A 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.196052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.174273 restraints weight = 6023.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.179745 restraints weight = 3771.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.183759 restraints weight = 2522.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.186443 restraints weight = 1757.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.188558 restraints weight = 1284.124| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3400 Z= 0.235 Angle : 0.870 13.657 4607 Z= 0.449 Chirality : 0.048 0.203 520 Planarity : 0.008 0.111 551 Dihedral : 7.774 82.073 447 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % 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: -0.25 (0.40), residues: 395 helix: 0.98 (0.33), residues: 218 sheet: -1.54 (0.64), residues: 54 loop : -1.50 (0.53), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 351 TYR 0.027 0.003 TYR A 94 PHE 0.025 0.003 PHE A 276 TRP 0.023 0.003 TRP A 252 HIS 0.008 0.003 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 ( 3398) covalent geometry : angle 0.86890 / 0.45 ( 4603) SS BOND : bond 0.01034 / 0.49 ( 2) SS BOND : angle 1.91798 / 1.05 ( 4) hydrogen bonds : bond 0.04851 / 3.08 ( 210) hydrogen bonds : angle 5.02566 / 3.41 ( 663) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7794 (p0) cc_final: 0.7443 (p0) REVERT: A 80 ILE cc_start: 0.8205 (mt) cc_final: 0.7532 (mt) REVERT: A 143 HIS cc_start: 0.6766 (m170) cc_final: 0.6513 (m-70) REVERT: A 182 TYR cc_start: 0.6330 (m-80) cc_final: 0.5598 (m-80) REVERT: A 206 PHE cc_start: 0.7388 (m-80) cc_final: 0.6931 (m-80) REVERT: A 227 MET cc_start: 0.8637 (tmm) cc_final: 0.8127 (tmm) REVERT: A 233 MET cc_start: 0.8904 (tpp) cc_final: 0.8202 (tmm) REVERT: A 270 MET cc_start: 0.5731 (mmp) cc_final: 0.5138 (mmt) REVERT: A 298 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7349 (tp30) REVERT: A 386 MET cc_start: 0.8340 (tpp) cc_final: 0.7946 (tpp) REVERT: A 387 LYS cc_start: 0.8889 (tptt) cc_final: 0.8516 (tttp) REVERT: A 435 TRP cc_start: 0.7896 (p-90) cc_final: 0.6866 (p-90) REVERT: A 451 MET cc_start: 0.7505 (mtt) cc_final: 0.7185 (mtp) REVERT: A 453 LEU cc_start: 0.8315 (mt) cc_final: 0.8055 (mt) REVERT: A 457 MET cc_start: 0.6644 (mtm) cc_final: 0.6024 (mtm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0490 time to fit residues: 6.4201 Evaluate side-chains 95 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 135 GLN A 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.198147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.171812 restraints weight = 5847.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.178051 restraints weight = 3580.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.182621 restraints weight = 2383.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.186010 restraints weight = 1671.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.188360 restraints weight = 1219.277| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5617 moved from start: 0.7731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3400 Z= 0.135 Angle : 0.629 11.037 4607 Z= 0.325 Chirality : 0.042 0.213 520 Planarity : 0.004 0.035 551 Dihedral : 7.052 79.089 447 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: 0.45 (0.42), residues: 395 helix: 1.62 (0.34), residues: 218 sheet: -1.38 (0.67), residues: 54 loop : -1.27 (0.56), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 39 TYR 0.021 0.002 TYR A 94 PHE 0.018 0.002 PHE A 184 TRP 0.011 0.001 TRP A 82 HIS 0.007 0.002 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 3398) covalent geometry : angle 0.62801 / 0.32 ( 4603) SS BOND : bond 0.00102 / 0.05 ( 2) SS BOND : angle 1.49627 / 0.84 ( 4) hydrogen bonds : bond 0.03976 / 2.54 ( 210) hydrogen bonds : angle 4.56604 / 3.12 ( 663) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ILE cc_start: 0.8386 (mt) cc_final: 0.7807 (mt) REVERT: A 227 MET cc_start: 0.8596 (tmm) cc_final: 0.8117 (tmm) REVERT: A 231 MET cc_start: 0.6338 (tpp) cc_final: 0.5941 (tpp) REVERT: A 233 MET cc_start: 0.8744 (tpp) cc_final: 0.8124 (tpp) REVERT: A 259 GLN cc_start: 0.8191 (mp10) cc_final: 0.7793 (mp10) REVERT: A 270 MET cc_start: 0.5552 (mmp) cc_final: 0.4889 (mmt) REVERT: A 298 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7483 (tp30) REVERT: A 386 MET cc_start: 0.8471 (tpp) cc_final: 0.8024 (tpp) REVERT: A 387 LYS cc_start: 0.8911 (tptt) cc_final: 0.8476 (tttp) REVERT: A 424 MET cc_start: 0.7357 (mmp) cc_final: 0.7124 (mmm) REVERT: A 434 ASP cc_start: 0.4683 (t0) cc_final: 0.4276 (t0) REVERT: A 442 ASP cc_start: 0.6530 (m-30) cc_final: 0.6127 (m-30) REVERT: A 453 LEU cc_start: 0.8498 (mt) cc_final: 0.8240 (mt) REVERT: A 457 MET cc_start: 0.6750 (mtm) cc_final: 0.6211 (mtm) REVERT: A 459 LEU cc_start: 0.6736 (mt) cc_final: 0.6396 (mt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0512 time to fit residues: 6.9369 Evaluate side-chains 94 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.0470 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 GLN A 356 GLN A 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.194022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.169200 restraints weight = 5938.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.175034 restraints weight = 3761.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.179358 restraints weight = 2525.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.182577 restraints weight = 1773.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.184773 restraints weight = 1296.772| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5775 moved from start: 0.9142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3400 Z= 0.169 Angle : 0.728 10.104 4607 Z= 0.376 Chirality : 0.045 0.211 520 Planarity : 0.005 0.049 551 Dihedral : 7.138 77.601 447 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.21 (0.42), residues: 395 helix: 1.29 (0.34), residues: 218 sheet: -1.01 (0.81), residues: 42 loop : -1.35 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 446 TYR 0.023 0.002 TYR A 94 PHE 0.024 0.002 PHE A 240 TRP 0.014 0.002 TRP A 252 HIS 0.006 0.002 HIS A 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 ( 3398) covalent geometry : angle 0.72449 / 0.37 ( 4603) SS BOND : bond 0.00116 / 0.06 ( 2) SS BOND : angle 2.66212 / 1.47 ( 4) hydrogen bonds : bond 0.04183 / 2.67 ( 210) hydrogen bonds : angle 4.70510 / 3.20 ( 663) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.8418 (tpp80) cc_final: 0.7584 (mmm160) REVERT: A 80 ILE cc_start: 0.8292 (mt) cc_final: 0.7848 (mt) REVERT: A 227 MET cc_start: 0.8536 (tmm) cc_final: 0.7979 (tmm) REVERT: A 231 MET cc_start: 0.6348 (tpp) cc_final: 0.5918 (tpp) REVERT: A 270 MET cc_start: 0.5867 (mmp) cc_final: 0.5315 (mmp) REVERT: A 298 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7492 (tp30) REVERT: A 386 MET cc_start: 0.8382 (tpp) cc_final: 0.8051 (tpp) REVERT: A 387 LYS cc_start: 0.8973 (tptt) cc_final: 0.8525 (tttp) REVERT: A 424 MET cc_start: 0.7185 (mmp) cc_final: 0.6972 (mmm) REVERT: A 436 ARG cc_start: 0.7679 (mpp-170) cc_final: 0.7365 (mpp80) REVERT: A 448 LEU cc_start: 0.9495 (pp) cc_final: 0.9162 (pp) REVERT: A 451 MET cc_start: 0.7853 (mtt) cc_final: 0.7157 (mtt) REVERT: A 453 LEU cc_start: 0.8544 (mt) cc_final: 0.8305 (mt) REVERT: A 457 MET cc_start: 0.6797 (mtm) cc_final: 0.6338 (mtm) REVERT: A 467 GLN cc_start: 0.7629 (tt0) cc_final: 0.7401 (tt0) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0482 time to fit residues: 6.5300 Evaluate side-chains 98 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 51 ASN A 135 GLN A 356 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.195245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.170862 restraints weight = 5909.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.176984 restraints weight = 3635.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.181274 restraints weight = 2402.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.184522 restraints weight = 1674.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.186725 restraints weight = 1208.570| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5788 moved from start: 0.9924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3400 Z= 0.158 Angle : 0.721 11.771 4607 Z= 0.367 Chirality : 0.044 0.164 520 Planarity : 0.004 0.040 551 Dihedral : 6.978 77.823 447 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 0.41 (0.42), residues: 395 helix: 1.52 (0.34), residues: 218 sheet: -1.39 (0.70), residues: 55 loop : -1.14 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 39 TYR 0.017 0.002 TYR A 277 PHE 0.045 0.002 PHE A 240 TRP 0.015 0.002 TRP A 82 HIS 0.003 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 3398) covalent geometry : angle 0.71757 / 0.37 ( 4603) SS BOND : bond 0.00228 / 0.11 ( 2) SS BOND : angle 2.61050 / 1.38 ( 4) hydrogen bonds : bond 0.04095 / 2.65 ( 210) hydrogen bonds : angle 4.58350 / 3.12 ( 663) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.8468 (tpp80) cc_final: 0.7713 (mmm160) REVERT: A 80 ILE cc_start: 0.8272 (mt) cc_final: 0.7649 (mt) REVERT: A 227 MET cc_start: 0.8457 (tmm) cc_final: 0.7973 (tmm) REVERT: A 231 MET cc_start: 0.6582 (tpp) cc_final: 0.6176 (tpp) REVERT: A 270 MET cc_start: 0.5725 (mmp) cc_final: 0.5507 (mmt) REVERT: A 288 GLU cc_start: 0.5392 (tt0) cc_final: 0.5135 (tt0) REVERT: A 298 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7570 (tp30) REVERT: A 386 MET cc_start: 0.8511 (tpp) cc_final: 0.8145 (tpp) REVERT: A 387 LYS cc_start: 0.8951 (tptt) cc_final: 0.8481 (tttp) REVERT: A 437 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6804 (mm-30) REVERT: A 448 LEU cc_start: 0.9499 (pp) cc_final: 0.9264 (pp) REVERT: A 451 MET cc_start: 0.7938 (mtt) cc_final: 0.7238 (mtt) REVERT: A 457 MET cc_start: 0.7392 (mtm) cc_final: 0.6998 (mtm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0544 time to fit residues: 7.1700 Evaluate side-chains 96 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.193960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.170883 restraints weight = 6049.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.176600 restraints weight = 3695.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.180754 restraints weight = 2452.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.183659 restraints weight = 1719.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.185964 restraints weight = 1260.396| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 1.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3400 Z= 0.159 Angle : 0.727 9.694 4607 Z= 0.375 Chirality : 0.044 0.153 520 Planarity : 0.005 0.049 551 Dihedral : 6.958 78.710 447 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 0.36 (0.42), residues: 395 helix: 1.39 (0.34), residues: 218 sheet: -0.97 (0.80), residues: 46 loop : -1.23 (0.51), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.017 0.002 TYR A 94 PHE 0.035 0.002 PHE A 240 TRP 0.017 0.002 TRP A 82 HIS 0.005 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 3398) covalent geometry : angle 0.72367 / 0.37 ( 4603) SS BOND : bond 0.00030 / 0.01 ( 2) SS BOND : angle 2.47543 / 1.34 ( 4) hydrogen bonds : bond 0.04141 / 2.63 ( 210) hydrogen bonds : angle 4.61112 / 3.15 ( 663) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.8363 (tpp80) cc_final: 0.7615 (mmm160) REVERT: A 80 ILE cc_start: 0.8306 (mt) cc_final: 0.7661 (mt) REVERT: A 84 LEU cc_start: 0.8546 (tp) cc_final: 0.8026 (tp) REVERT: A 95 ASN cc_start: 0.9158 (m-40) cc_final: 0.8832 (m110) REVERT: A 107 LYS cc_start: 0.8217 (mppt) cc_final: 0.7777 (mppt) REVERT: A 143 HIS cc_start: 0.5970 (m-70) cc_final: 0.5204 (t-90) REVERT: A 227 MET cc_start: 0.8444 (tmm) cc_final: 0.7959 (tmm) REVERT: A 231 MET cc_start: 0.6421 (tpp) cc_final: 0.6106 (tpp) REVERT: A 386 MET cc_start: 0.8470 (tpp) cc_final: 0.8140 (tpp) REVERT: A 387 LYS cc_start: 0.8863 (tptt) cc_final: 0.8450 (tttp) REVERT: A 408 LEU cc_start: 0.8276 (mt) cc_final: 0.8061 (mt) REVERT: A 424 MET cc_start: 0.7033 (mmp) cc_final: 0.6811 (mmm) REVERT: A 451 MET cc_start: 0.7999 (mtt) cc_final: 0.7337 (mtt) REVERT: A 453 LEU cc_start: 0.8563 (mt) cc_final: 0.8334 (mt) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.0429 time to fit residues: 5.5558 Evaluate side-chains 89 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 135 GLN A 356 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.196474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.172287 restraints weight = 5927.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.178391 restraints weight = 3623.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.182759 restraints weight = 2393.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.185890 restraints weight = 1665.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.188295 restraints weight = 1206.580| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5827 moved from start: 1.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3400 Z= 0.134 Angle : 0.681 9.537 4607 Z= 0.349 Chirality : 0.043 0.172 520 Planarity : 0.004 0.041 551 Dihedral : 6.735 79.044 447 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 0.51 (0.43), residues: 395 helix: 1.55 (0.34), residues: 218 sheet: -1.19 (0.70), residues: 55 loop : -1.07 (0.57), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 436 TYR 0.026 0.002 TYR A 94 PHE 0.036 0.002 PHE A 240 TRP 0.018 0.001 TRP A 82 HIS 0.005 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 3398) covalent geometry : angle 0.67769 / 0.35 ( 4603) SS BOND : bond 0.00389 / 0.19 ( 2) SS BOND : angle 2.28570 / 1.23 ( 4) hydrogen bonds : bond 0.03873 / 2.51 ( 210) hydrogen bonds : angle 4.43302 / 3.03 ( 663) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7753 (p0) cc_final: 0.7506 (p0) REVERT: A 80 ILE cc_start: 0.8361 (mt) cc_final: 0.7914 (mt) REVERT: A 84 LEU cc_start: 0.8450 (tp) cc_final: 0.8021 (tp) REVERT: A 107 LYS cc_start: 0.8307 (mppt) cc_final: 0.7946 (mppt) REVERT: A 227 MET cc_start: 0.8370 (tmm) cc_final: 0.7890 (tmm) REVERT: A 270 MET cc_start: 0.4687 (mmt) cc_final: 0.4353 (mmt) REVERT: A 298 GLU cc_start: 0.7752 (tp30) cc_final: 0.7516 (tp30) REVERT: A 386 MET cc_start: 0.8723 (tpp) cc_final: 0.8136 (tpp) REVERT: A 387 LYS cc_start: 0.8839 (tptt) cc_final: 0.8411 (tttp) REVERT: A 424 MET cc_start: 0.6744 (mmp) cc_final: 0.6452 (mmm) REVERT: A 436 ARG cc_start: 0.8055 (mmm-85) cc_final: 0.7532 (mmm-85) REVERT: A 447 LEU cc_start: 0.8315 (tp) cc_final: 0.8098 (tp) REVERT: A 451 MET cc_start: 0.8059 (mtt) cc_final: 0.7449 (mtt) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.0405 time to fit residues: 5.3572 Evaluate side-chains 88 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.197049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.172201 restraints weight = 5934.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.178303 restraints weight = 3700.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.182802 restraints weight = 2467.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.186009 restraints weight = 1727.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.188465 restraints weight = 1255.664| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 moved from start: 1.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3400 Z= 0.140 Angle : 0.698 9.118 4607 Z= 0.360 Chirality : 0.043 0.151 520 Planarity : 0.004 0.040 551 Dihedral : 6.774 79.495 447 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 0.57 (0.43), residues: 395 helix: 1.59 (0.34), residues: 218 sheet: -1.30 (0.76), residues: 47 loop : -1.02 (0.56), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.021 0.002 TYR A 94 PHE 0.033 0.002 PHE A 240 TRP 0.018 0.001 TRP A 82 HIS 0.002 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 3398) covalent geometry : angle 0.69484 / 0.36 ( 4603) SS BOND : bond 0.00069 / 0.03 ( 2) SS BOND : angle 2.19673 / 1.15 ( 4) hydrogen bonds : bond 0.04004 / 2.60 ( 210) hydrogen bonds : angle 4.44815 / 3.05 ( 663) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8083 (mmmm) cc_final: 0.7692 (mmmt) REVERT: A 80 ILE cc_start: 0.8406 (mt) cc_final: 0.8017 (mt) REVERT: A 84 LEU cc_start: 0.8373 (tp) cc_final: 0.7987 (tp) REVERT: A 107 LYS cc_start: 0.8267 (mppt) cc_final: 0.7905 (mppt) REVERT: A 227 MET cc_start: 0.8113 (tmm) cc_final: 0.7699 (tmm) REVERT: A 305 ARG cc_start: 0.6887 (ptt-90) cc_final: 0.5761 (ttm110) REVERT: A 386 MET cc_start: 0.8649 (tpp) cc_final: 0.8082 (tpp) REVERT: A 387 LYS cc_start: 0.8821 (tptt) cc_final: 0.8438 (tttp) REVERT: A 424 MET cc_start: 0.6547 (mmp) cc_final: 0.6244 (mmm) REVERT: A 436 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.7406 (mmm-85) REVERT: A 447 LEU cc_start: 0.8316 (tp) cc_final: 0.8074 (tp) REVERT: A 451 MET cc_start: 0.7977 (mtt) cc_final: 0.7343 (mtt) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0412 time to fit residues: 5.8717 Evaluate side-chains 98 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 GLN A 356 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.189752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.164686 restraints weight = 5824.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.170629 restraints weight = 3531.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.175087 restraints weight = 2362.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.178242 restraints weight = 1662.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.180251 restraints weight = 1223.699| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 1.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3400 Z= 0.162 Angle : 0.742 8.790 4607 Z= 0.384 Chirality : 0.043 0.147 520 Planarity : 0.004 0.041 551 Dihedral : 6.997 81.005 447 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: 0.29 (0.42), residues: 395 helix: 1.23 (0.33), residues: 218 sheet: -0.93 (0.71), residues: 53 loop : -1.06 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 305 TYR 0.022 0.002 TYR A 94 PHE 0.027 0.002 PHE A 240 TRP 0.019 0.002 TRP A 82 HIS 0.003 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 3398) covalent geometry : angle 0.73902 / 0.38 ( 4603) SS BOND : bond 0.00109 / 0.05 ( 2) SS BOND : angle 2.18752 / 1.15 ( 4) hydrogen bonds : bond 0.04226 / 2.73 ( 210) hydrogen bonds : angle 4.53615 / 3.11 ( 663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 558.95 seconds wall clock time: 10 minutes 12.78 seconds (612.78 seconds total)