Starting phenix.real_space_refine on Fri Aug 22 13:26:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jts_36651/08_2025/8jts_36651.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jts_36651/08_2025/8jts_36651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jts_36651/08_2025/8jts_36651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jts_36651/08_2025/8jts_36651.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jts_36651/08_2025/8jts_36651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jts_36651/08_2025/8jts_36651.map" } resolution = 4.14 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= 0.002 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 2190 2.51 5 N 534 2.21 5 O 583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3330 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3321 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 20, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 7, 'PHE:plan': 3, 'HIS:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 3, 'ARG:plan': 9, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 157 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.99, per 1000 atoms: 0.30 Number of scatterers: 3330 At special positions: 0 Unit cell: (94.1775, 58.455, 67.115, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 583 8.00 N 534 7.00 C 2190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 141.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 850 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 77.0% alpha, 0.0% 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 3 through 12 Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 32 through 37 removed outlier: 3.670A pdb=" N CYS A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 146 through 166 Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 174 through 195 Processing helix chain 'A' and resid 199 through 228 Processing helix chain 'A' and resid 232 through 258 Processing helix chain 'A' and resid 260 through 279 removed outlier: 3.668A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.896A pdb=" N TYR A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 340 through 368 Processing helix chain 'A' and resid 376 through 397 removed outlier: 3.657A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 403 through 423 removed outlier: 3.865A pdb=" N MET A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 456 removed outlier: 4.146A pdb=" N ILE A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 removed outlier: 4.081A pdb=" N ASN A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.855A pdb=" N CYS A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 491 Proline residue: A 481 - end of helix removed outlier: 3.888A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 510 removed outlier: 3.676A pdb=" N ILE A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.986A pdb=" N LEU A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 714 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: 0.54 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 533 1.30 - 1.43: 891 1.43 - 1.56: 1950 1.56 - 1.69: 0 1.69 - 1.82: 35 Bond restraints: 3409 Sorted by residual: bond pdb=" CA THR A 356 " pdb=" C THR A 356 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.27e-02 6.20e+03 7.52e+01 bond pdb=" C07 MF8 A 601 " pdb=" N08 MF8 A 601 " ideal model delta sigma weight residual 1.281 1.447 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" N ARG A 439 " pdb=" CA ARG A 439 " ideal model delta sigma weight residual 1.459 1.363 0.095 1.24e-02 6.50e+03 5.90e+01 bond pdb=" C07 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.393 1.245 0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" CA ASP A 357 " pdb=" CB ASP A 357 " ideal model delta sigma weight residual 1.530 1.432 0.098 1.57e-02 4.06e+03 3.91e+01 ... (remaining 3404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 4485 1.96 - 3.91: 134 3.91 - 5.87: 39 5.87 - 7.82: 12 7.82 - 9.78: 6 Bond angle restraints: 4676 Sorted by residual: angle pdb=" N THR A 356 " pdb=" CA THR A 356 " pdb=" C THR A 356 " ideal model delta sigma weight residual 111.07 102.52 8.55 1.07e+00 8.73e-01 6.38e+01 angle pdb=" C THR A 356 " pdb=" N ASP A 357 " pdb=" CA ASP A 357 " ideal model delta sigma weight residual 120.65 110.87 9.78 1.32e+00 5.74e-01 5.49e+01 angle pdb=" CA ASP A 357 " pdb=" C ASP A 357 " pdb=" N SER A 358 " ideal model delta sigma weight residual 116.92 124.94 -8.02 1.16e+00 7.43e-01 4.79e+01 angle pdb=" N GLN A 362 " pdb=" CA GLN A 362 " pdb=" C GLN A 362 " ideal model delta sigma weight residual 111.75 104.24 7.51 1.28e+00 6.10e-01 3.44e+01 angle pdb=" O ASP A 357 " pdb=" C ASP A 357 " pdb=" N SER A 358 " ideal model delta sigma weight residual 122.03 116.89 5.14 1.04e+00 9.25e-01 2.44e+01 ... (remaining 4671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 1767 17.47 - 34.94: 148 34.94 - 52.41: 29 52.41 - 69.89: 7 69.89 - 87.36: 3 Dihedral angle restraints: 1954 sinusoidal: 634 harmonic: 1320 Sorted by residual: dihedral pdb=" CA ILE A 442 " pdb=" C ILE A 442 " pdb=" N THR A 443 " pdb=" CA THR A 443 " ideal model delta harmonic sigma weight residual 180.00 151.77 28.23 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA THR A 356 " pdb=" C THR A 356 " pdb=" N ASP A 357 " pdb=" CA ASP A 357 " ideal model delta harmonic sigma weight residual 180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA MET A 448 " pdb=" C MET A 448 " pdb=" N ILE A 449 " pdb=" CA ILE A 449 " ideal model delta harmonic sigma weight residual 180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 1951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 465 0.056 - 0.112: 92 0.112 - 0.168: 8 0.168 - 0.224: 2 0.224 - 0.280: 4 Chirality restraints: 571 Sorted by residual: chirality pdb=" CG LEU A 25 " pdb=" CB LEU A 25 " pdb=" CD1 LEU A 25 " pdb=" CD2 LEU A 25 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ASP A 357 " pdb=" N ASP A 357 " pdb=" C ASP A 357 " pdb=" CB ASP A 357 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA TYR A 361 " pdb=" N TYR A 361 " pdb=" C TYR A 361 " pdb=" CB TYR A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 568 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 601 " -0.070 2.00e-02 2.50e+03 4.80e-01 5.19e+03 pdb=" C03 MF8 A 601 " 0.458 2.00e-02 2.50e+03 pdb=" C04 MF8 A 601 " -0.216 2.00e-02 2.50e+03 pdb=" C07 MF8 A 601 " 0.227 2.00e-02 2.50e+03 pdb=" N02 MF8 A 601 " 0.055 2.00e-02 2.50e+03 pdb=" N05 MF8 A 601 " -1.078 2.00e-02 2.50e+03 pdb=" N06 MF8 A 601 " 0.514 2.00e-02 2.50e+03 pdb=" N08 MF8 A 601 " -0.349 2.00e-02 2.50e+03 pdb=" N09 MF8 A 601 " 0.459 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.044 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO A 271 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 361 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C TYR A 361 " 0.041 2.00e-02 2.50e+03 pdb=" O TYR A 361 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN A 362 " -0.014 2.00e-02 2.50e+03 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 738 2.78 - 3.31: 3476 3.31 - 3.84: 5593 3.84 - 4.37: 5722 4.37 - 4.90: 9809 Nonbonded interactions: 25338 Sorted by model distance: nonbonded pdb=" O GLY A 167 " pdb=" ND2 ASN A 463 " model vdw 2.249 3.120 nonbonded pdb=" OG SER A 424 " pdb=" OD1 ASP A 426 " model vdw 2.315 3.040 nonbonded pdb=" O GLY A 12 " pdb=" NE2 GLN A 18 " model vdw 2.327 3.120 nonbonded pdb=" OD1 ASN A 198 " pdb=" OG SER A 201 " model vdw 2.345 3.040 nonbonded pdb=" O VAL A 141 " pdb=" OG SER A 145 " model vdw 2.367 3.040 ... (remaining 25333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.580 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 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 : 0.008 0.166 3409 Z= 0.495 Angle : 0.933 9.780 4676 Z= 0.539 Chirality : 0.049 0.280 571 Planarity : 0.021 0.480 582 Dihedral : 14.111 87.356 1104 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.31 % Allowed : 0.94 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.39), residues: 457 helix: 0.25 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.17 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 439 TYR 0.010 0.001 TYR A 256 PHE 0.021 0.002 PHE A 151 TRP 0.007 0.001 TRP A 354 HIS 0.001 0.000 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00800 ( 3409) covalent geometry : angle 0.93290 ( 4676) hydrogen bonds : bond 0.12925 ( 238) hydrogen bonds : angle 6.11926 ( 714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.124 Fit side-chains REVERT: A 137 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6584 (mm-30) REVERT: A 293 LYS cc_start: 0.8310 (mttm) cc_final: 0.8109 (mttm) REVERT: A 352 TYR cc_start: 0.5406 (m-80) cc_final: 0.5079 (m-80) REVERT: A 361 TYR cc_start: 0.8688 (t80) cc_final: 0.8330 (t80) REVERT: A 449 ILE cc_start: 0.8890 (tt) cc_final: 0.8569 (tt) outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.0456 time to fit residues: 5.6745 Evaluate side-chains 80 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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: 8.9990 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.215141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.188764 restraints weight = 4755.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.193572 restraints weight = 2677.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.196845 restraints weight = 1745.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.198803 restraints weight = 1288.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.200581 restraints weight = 1042.036| |-----------------------------------------------------------------------------| r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3409 Z= 0.141 Angle : 0.606 6.755 4676 Z= 0.306 Chirality : 0.040 0.164 571 Planarity : 0.005 0.063 582 Dihedral : 4.454 19.764 479 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.31 % Allowed : 6.56 % Favored : 93.12 % 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 aren not related in a simple way. whole: 0.29 (0.40), residues: 457 helix: 0.75 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.12 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.012 0.001 TYR A 256 PHE 0.021 0.002 PHE A 41 TRP 0.007 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3409) covalent geometry : angle 0.60585 ( 4676) hydrogen bonds : bond 0.04828 ( 238) hydrogen bonds : angle 5.07650 ( 714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.101 Fit side-chains REVERT: A 137 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6607 (mm-30) REVERT: A 352 TYR cc_start: 0.5612 (m-80) cc_final: 0.5385 (m-80) REVERT: A 449 ILE cc_start: 0.8886 (tt) cc_final: 0.8546 (tt) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.0376 time to fit residues: 5.0627 Evaluate side-chains 81 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 0.0570 chunk 29 optimal weight: 0.0670 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 0.0470 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS A 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.218847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.193428 restraints weight = 4694.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.198200 restraints weight = 2621.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.201137 restraints weight = 1697.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.203775 restraints weight = 1258.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.205107 restraints weight = 992.962| |-----------------------------------------------------------------------------| r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3409 Z= 0.123 Angle : 0.611 7.366 4676 Z= 0.295 Chirality : 0.039 0.142 571 Planarity : 0.005 0.059 582 Dihedral : 4.212 16.788 479 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.40), residues: 457 helix: 1.11 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -1.00 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.015 0.001 TYR A 361 PHE 0.014 0.001 PHE A 41 TRP 0.009 0.001 TRP A 261 HIS 0.001 0.000 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3409) covalent geometry : angle 0.61066 ( 4676) hydrogen bonds : bond 0.04436 ( 238) hydrogen bonds : angle 4.92875 ( 714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.124 Fit side-chains REVERT: A 137 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6601 (mm-30) REVERT: A 287 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.8189 (ttm-80) REVERT: A 426 ASP cc_start: 0.7837 (p0) cc_final: 0.7282 (m-30) REVERT: A 449 ILE cc_start: 0.8746 (tt) cc_final: 0.8469 (tt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0439 time to fit residues: 5.5397 Evaluate side-chains 82 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 26 optimal weight: 0.0770 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.213662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.187821 restraints weight = 4759.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.192510 restraints weight = 2663.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.195360 restraints weight = 1742.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.198045 restraints weight = 1298.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.199315 restraints weight = 1025.008| |-----------------------------------------------------------------------------| r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3409 Z= 0.137 Angle : 0.613 7.109 4676 Z= 0.305 Chirality : 0.040 0.193 571 Planarity : 0.005 0.062 582 Dihedral : 4.200 16.183 479 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.31 % Allowed : 5.00 % Favored : 94.69 % 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 aren not related in a simple way. whole: 0.84 (0.40), residues: 457 helix: 1.17 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.00 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.012 0.001 TYR A 256 PHE 0.020 0.002 PHE A 151 TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3409) covalent geometry : angle 0.61320 ( 4676) hydrogen bonds : bond 0.04532 ( 238) hydrogen bonds : angle 4.94744 ( 714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.079 Fit side-chains REVERT: A 137 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6436 (mm-30) REVERT: A 426 ASP cc_start: 0.7897 (p0) cc_final: 0.7347 (m-30) REVERT: A 449 ILE cc_start: 0.8812 (tt) cc_final: 0.8551 (tt) outliers start: 1 outliers final: 1 residues processed: 97 average time/residue: 0.0423 time to fit residues: 5.4060 Evaluate side-chains 86 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 20 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.218069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.194624 restraints weight = 4648.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.198857 restraints weight = 2654.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.201572 restraints weight = 1762.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.203943 restraints weight = 1321.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.204969 restraints weight = 1055.969| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3409 Z= 0.127 Angle : 0.611 6.863 4676 Z= 0.300 Chirality : 0.039 0.168 571 Planarity : 0.005 0.059 582 Dihedral : 4.175 15.667 479 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.40), residues: 457 helix: 1.25 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.10 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.010 0.001 TYR A 361 PHE 0.019 0.001 PHE A 41 TRP 0.007 0.001 TRP A 217 HIS 0.001 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3409) covalent geometry : angle 0.61115 ( 4676) hydrogen bonds : bond 0.04373 ( 238) hydrogen bonds : angle 4.94719 ( 714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.187 Fit side-chains REVERT: A 137 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6441 (mm-30) REVERT: A 287 ARG cc_start: 0.8675 (ttm-80) cc_final: 0.8386 (ttm-80) REVERT: A 352 TYR cc_start: 0.5387 (m-80) cc_final: 0.5172 (m-80) REVERT: A 426 ASP cc_start: 0.8278 (p0) cc_final: 0.7764 (m-30) REVERT: A 449 ILE cc_start: 0.8812 (tt) cc_final: 0.8517 (tt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0388 time to fit residues: 4.8950 Evaluate side-chains 83 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.1980 chunk 34 optimal weight: 0.0270 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.0970 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.214320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.190834 restraints weight = 4713.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.195427 restraints weight = 2634.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.198380 restraints weight = 1699.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.200568 restraints weight = 1235.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.201829 restraints weight = 977.508| |-----------------------------------------------------------------------------| r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3409 Z= 0.123 Angle : 0.615 7.417 4676 Z= 0.300 Chirality : 0.039 0.157 571 Planarity : 0.004 0.058 582 Dihedral : 4.100 14.819 479 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.40), residues: 457 helix: 1.31 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.07 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.010 0.001 TYR A 361 PHE 0.023 0.001 PHE A 151 TRP 0.007 0.001 TRP A 217 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3409) covalent geometry : angle 0.61523 ( 4676) hydrogen bonds : bond 0.04227 ( 238) hydrogen bonds : angle 5.00788 ( 714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.137 Fit side-chains REVERT: A 137 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6371 (mm-30) REVERT: A 287 ARG cc_start: 0.8694 (ttm-80) cc_final: 0.8356 (ttm-80) REVERT: A 426 ASP cc_start: 0.8277 (p0) cc_final: 0.7765 (m-30) REVERT: A 449 ILE cc_start: 0.8809 (tt) cc_final: 0.8492 (tt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0477 time to fit residues: 5.9519 Evaluate side-chains 87 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.213198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.189798 restraints weight = 4796.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.194191 restraints weight = 2668.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.197355 restraints weight = 1722.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.199705 restraints weight = 1237.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.201028 restraints weight = 967.749| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3409 Z= 0.124 Angle : 0.619 7.681 4676 Z= 0.303 Chirality : 0.040 0.228 571 Planarity : 0.004 0.057 582 Dihedral : 4.083 14.630 479 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.40), residues: 457 helix: 1.39 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.07 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.009 0.001 TYR A 361 PHE 0.017 0.001 PHE A 41 TRP 0.007 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3409) covalent geometry : angle 0.61861 ( 4676) hydrogen bonds : bond 0.04217 ( 238) hydrogen bonds : angle 4.99946 ( 714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.128 Fit side-chains REVERT: A 137 GLU cc_start: 0.6687 (mm-30) cc_final: 0.6425 (mm-30) REVERT: A 287 ARG cc_start: 0.8695 (ttm-80) cc_final: 0.8373 (ttm-80) REVERT: A 361 TYR cc_start: 0.7995 (t80) cc_final: 0.7532 (t80) REVERT: A 426 ASP cc_start: 0.8287 (p0) cc_final: 0.7763 (m-30) REVERT: A 449 ILE cc_start: 0.8815 (tt) cc_final: 0.8505 (tt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0494 time to fit residues: 6.1948 Evaluate side-chains 89 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 0.0370 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.216377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.190602 restraints weight = 4841.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.195681 restraints weight = 2668.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.199203 restraints weight = 1706.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.201209 restraints weight = 1225.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.203265 restraints weight = 977.942| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3409 Z= 0.128 Angle : 0.644 7.767 4676 Z= 0.315 Chirality : 0.040 0.204 571 Planarity : 0.005 0.058 582 Dihedral : 4.022 15.198 479 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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 aren not related in a simple way. whole: 1.07 (0.41), residues: 457 helix: 1.37 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.05 (0.60), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.010 0.001 TYR A 256 PHE 0.024 0.002 PHE A 151 TRP 0.005 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 3409) covalent geometry : angle 0.64389 ( 4676) hydrogen bonds : bond 0.04283 ( 238) hydrogen bonds : angle 5.04293 ( 714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.131 Fit side-chains REVERT: A 137 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6471 (mm-30) REVERT: A 287 ARG cc_start: 0.8763 (ttm-80) cc_final: 0.8437 (ttm-80) REVERT: A 426 ASP cc_start: 0.8312 (p0) cc_final: 0.7780 (m-30) REVERT: A 449 ILE cc_start: 0.8830 (tt) cc_final: 0.8507 (tt) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0476 time to fit residues: 5.9324 Evaluate side-chains 88 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.215772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.189708 restraints weight = 4748.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.194660 restraints weight = 2646.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.198206 restraints weight = 1706.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.200307 restraints weight = 1236.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.202250 restraints weight = 987.833| |-----------------------------------------------------------------------------| r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3409 Z= 0.131 Angle : 0.642 7.674 4676 Z= 0.316 Chirality : 0.040 0.215 571 Planarity : 0.005 0.058 582 Dihedral : 4.073 15.053 479 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.41), residues: 457 helix: 1.42 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.07 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 175 TYR 0.010 0.001 TYR A 256 PHE 0.018 0.001 PHE A 41 TRP 0.007 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3409) covalent geometry : angle 0.64205 ( 4676) hydrogen bonds : bond 0.04339 ( 238) hydrogen bonds : angle 5.03092 ( 714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.122 Fit side-chains REVERT: A 287 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8460 (ttm-80) REVERT: A 352 TYR cc_start: 0.5388 (m-80) cc_final: 0.5100 (m-80) REVERT: A 426 ASP cc_start: 0.8323 (p0) cc_final: 0.7804 (m-30) REVERT: A 449 ILE cc_start: 0.8842 (tt) cc_final: 0.8538 (tt) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0367 time to fit residues: 4.6885 Evaluate side-chains 87 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 7 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.0030 chunk 30 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.215568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.189281 restraints weight = 4821.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.194328 restraints weight = 2625.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.197454 restraints weight = 1676.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.200292 restraints weight = 1223.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.201367 restraints weight = 951.349| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3409 Z= 0.131 Angle : 0.656 7.965 4676 Z= 0.322 Chirality : 0.041 0.210 571 Planarity : 0.005 0.058 582 Dihedral : 4.053 15.651 479 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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 aren not related in a simple way. whole: 1.16 (0.40), residues: 457 helix: 1.44 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.00 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.009 0.001 TYR A 256 PHE 0.023 0.001 PHE A 151 TRP 0.007 0.001 TRP A 217 HIS 0.001 0.000 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3409) covalent geometry : angle 0.65635 ( 4676) hydrogen bonds : bond 0.04339 ( 238) hydrogen bonds : angle 5.09135 ( 714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.133 Fit side-chains REVERT: A 287 ARG cc_start: 0.8789 (ttm-80) cc_final: 0.8448 (ttm-80) REVERT: A 426 ASP cc_start: 0.8372 (p0) cc_final: 0.7865 (m-30) REVERT: A 449 ILE cc_start: 0.8849 (tt) cc_final: 0.8614 (tt) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0364 time to fit residues: 4.7221 Evaluate side-chains 90 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 22 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.210612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.187231 restraints weight = 4749.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.191701 restraints weight = 2610.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.194992 restraints weight = 1676.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.197065 restraints weight = 1202.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.198801 restraints weight = 954.672| |-----------------------------------------------------------------------------| r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3409 Z= 0.142 Angle : 0.666 7.643 4676 Z= 0.333 Chirality : 0.042 0.226 571 Planarity : 0.005 0.057 582 Dihedral : 4.181 16.563 479 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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 aren not related in a simple way. whole: 1.11 (0.41), residues: 457 helix: 1.41 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.04 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 175 TYR 0.011 0.001 TYR A 256 PHE 0.019 0.002 PHE A 41 TRP 0.018 0.001 TRP A 288 HIS 0.001 0.000 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3409) covalent geometry : angle 0.66569 ( 4676) hydrogen bonds : bond 0.04471 ( 238) hydrogen bonds : angle 5.11474 ( 714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 703.31 seconds wall clock time: 12 minutes 47.38 seconds (767.38 seconds total)