Starting phenix.real_space_refine on Fri May 9 18:05:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p6a_17462/05_2025/8p6a_17462.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p6a_17462/05_2025/8p6a_17462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p6a_17462/05_2025/8p6a_17462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p6a_17462/05_2025/8p6a_17462.map" model { file = "/net/cci-nas-00/data/ceres_data/8p6a_17462/05_2025/8p6a_17462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p6a_17462/05_2025/8p6a_17462.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.048 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 16 5.16 5 C 2225 2.51 5 N 531 2.21 5 O 565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3337 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3337 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 15, 'TRANS': 416} Chain breaks: 3 Time building chain proxies: 2.81, per 1000 atoms: 0.84 Number of scatterers: 3337 At special positions: 0 Unit cell: (72.384, 67.392, 65.728, 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 16 16.00 O 565 8.00 N 531 7.00 C 2225 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: 0.82 Conformation dependent library (CDL) restraints added in 514.7 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 790 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 1 sheets defined 80.6% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 35 through 62 removed outlier: 5.178A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 96 removed outlier: 3.984A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 157 through 182 removed outlier: 4.188A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 183 through 186 Processing helix chain 'A' and resid 187 through 220 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.685A pdb=" N THR A 224 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 244 Processing helix chain 'A' and resid 311 through 346 removed outlier: 3.690A pdb=" N VAL A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 367 through 370 removed outlier: 3.915A pdb=" N THR A 370 " --> pdb=" O ALA A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 370' Processing helix chain 'A' and resid 371 through 396 Proline residue: A 382 - end of helix Proline residue: A 390 - end of helix Processing helix chain 'A' and resid 400 through 433 removed outlier: 3.632A pdb=" N ARG A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 Processing helix chain 'A' and resid 454 through 479 removed outlier: 4.047A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 511 Processing helix chain 'A' and resid 532 through 559 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 258 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1002 1.34 - 1.46: 751 1.46 - 1.58: 1641 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3420 Sorted by residual: bond pdb=" CA VAL A 322 " pdb=" C VAL A 322 " ideal model delta sigma weight residual 1.520 1.532 -0.013 8.80e-03 1.29e+04 2.04e+00 bond pdb=" CB ASP A 185 " pdb=" CG ASP A 185 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.21e+00 bond pdb=" CB ASP A 97 " pdb=" CG ASP A 97 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.20e+00 bond pdb=" C ALA A 65 " pdb=" N PRO A 66 " ideal model delta sigma weight residual 1.340 1.367 -0.027 2.76e-02 1.31e+03 9.38e-01 bond pdb=" CG LEU A 46 " pdb=" CD2 LEU A 46 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.25e-01 ... (remaining 3415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 4591 2.31 - 4.62: 40 4.62 - 6.93: 12 6.93 - 9.24: 4 9.24 - 11.55: 1 Bond angle restraints: 4648 Sorted by residual: angle pdb=" CB MET A 117 " pdb=" CG MET A 117 " pdb=" SD MET A 117 " ideal model delta sigma weight residual 112.70 124.25 -11.55 3.00e+00 1.11e-01 1.48e+01 angle pdb=" CA LEU A 344 " pdb=" CB LEU A 344 " pdb=" CG LEU A 344 " ideal model delta sigma weight residual 116.30 125.21 -8.91 3.50e+00 8.16e-02 6.48e+00 angle pdb=" CA LEU A 79 " pdb=" CB LEU A 79 " pdb=" CG LEU A 79 " ideal model delta sigma weight residual 116.30 124.51 -8.21 3.50e+00 8.16e-02 5.50e+00 angle pdb=" CA LEU A 507 " pdb=" CB LEU A 507 " pdb=" CG LEU A 507 " ideal model delta sigma weight residual 116.30 123.81 -7.51 3.50e+00 8.16e-02 4.61e+00 angle pdb=" CA LEU A 42 " pdb=" CB LEU A 42 " pdb=" CG LEU A 42 " ideal model delta sigma weight residual 116.30 123.70 -7.40 3.50e+00 8.16e-02 4.47e+00 ... (remaining 4643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 1602 15.10 - 30.19: 252 30.19 - 45.29: 75 45.29 - 60.38: 30 60.38 - 75.48: 4 Dihedral angle restraints: 1963 sinusoidal: 729 harmonic: 1234 Sorted by residual: dihedral pdb=" CG ARG A 193 " pdb=" CD ARG A 193 " pdb=" NE ARG A 193 " pdb=" CZ ARG A 193 " ideal model delta sinusoidal sigma weight residual 180.00 135.59 44.41 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG A 404 " pdb=" CD ARG A 404 " pdb=" NE ARG A 404 " pdb=" CZ ARG A 404 " ideal model delta sinusoidal sigma weight residual -180.00 -137.22 -42.78 2 1.50e+01 4.44e-03 9.84e+00 dihedral pdb=" CB ARG A 404 " pdb=" CG ARG A 404 " pdb=" CD ARG A 404 " pdb=" NE ARG A 404 " ideal model delta sinusoidal sigma weight residual 180.00 122.86 57.14 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 1960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 401 0.043 - 0.086: 118 0.086 - 0.129: 20 0.129 - 0.173: 4 0.173 - 0.216: 1 Chirality restraints: 544 Sorted by residual: chirality pdb=" CB ILE A 329 " pdb=" CA ILE A 329 " pdb=" CG1 ILE A 329 " pdb=" CG2 ILE A 329 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB VAL A 246 " pdb=" CA VAL A 246 " pdb=" CG1 VAL A 246 " pdb=" CG2 VAL A 246 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA VAL A 455 " pdb=" N VAL A 455 " pdb=" C VAL A 455 " pdb=" CB VAL A 455 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 541 not shown) Planarity restraints: 567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 457 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" CD GLN A 457 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLN A 457 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN A 457 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 455 " -0.023 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO A 456 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 385 " -0.005 2.00e-02 2.50e+03 1.10e-02 1.20e+00 pdb=" C ASP A 385 " 0.019 2.00e-02 2.50e+03 pdb=" O ASP A 385 " -0.007 2.00e-02 2.50e+03 pdb=" N LYS A 386 " -0.006 2.00e-02 2.50e+03 ... (remaining 564 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 82 2.71 - 3.26: 3478 3.26 - 3.80: 5677 3.80 - 4.35: 6172 4.35 - 4.90: 10711 Nonbonded interactions: 26120 Sorted by model distance: nonbonded pdb=" OG SER A 415 " pdb=" OE1 GLN A 457 " model vdw 2.161 3.040 nonbonded pdb=" O SER A 415 " pdb=" NE2 GLN A 457 " model vdw 2.239 3.120 nonbonded pdb=" OH TYR A 342 " pdb=" OE1 GLN A 457 " model vdw 2.302 3.040 nonbonded pdb=" O ARG A 394 " pdb=" NH1 ARG A 394 " model vdw 2.372 3.120 nonbonded pdb=" OG SER A 109 " pdb=" O GLY A 167 " model vdw 2.394 3.040 ... (remaining 26115 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: 1.650 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.740 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3420 Z= 0.142 Angle : 0.656 11.546 4648 Z= 0.313 Chirality : 0.041 0.216 544 Planarity : 0.003 0.034 567 Dihedral : 17.396 75.475 1173 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.29 % Allowed : 39.48 % Favored : 60.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.43), residues: 424 helix: 2.59 (0.29), residues: 325 sheet: -1.95 (1.74), residues: 10 loop : -0.54 (0.73), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 368 HIS 0.002 0.000 HIS A 348 PHE 0.013 0.001 PHE A 247 TYR 0.013 0.001 TYR A 444 ARG 0.001 0.000 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.09273 ( 258) hydrogen bonds : angle 4.28419 ( 762) covalent geometry : bond 0.00304 ( 3420) covalent geometry : angle 0.65646 ( 4648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.341 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.1353 time to fit residues: 12.5102 Evaluate side-chains 73 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.0060 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 0.0980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.155010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128154 restraints weight = 5337.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131930 restraints weight = 2875.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134311 restraints weight = 2012.588| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3420 Z= 0.126 Angle : 0.557 7.239 4648 Z= 0.274 Chirality : 0.039 0.150 544 Planarity : 0.003 0.035 567 Dihedral : 3.875 29.691 459 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.75 % Allowed : 34.58 % Favored : 61.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.42), residues: 424 helix: 2.70 (0.28), residues: 325 sheet: -2.27 (1.59), residues: 10 loop : -0.78 (0.72), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.003 0.001 HIS A 348 PHE 0.012 0.001 PHE A 247 TYR 0.014 0.001 TYR A 444 ARG 0.001 0.000 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 258) hydrogen bonds : angle 3.90381 ( 762) covalent geometry : bond 0.00260 ( 3420) covalent geometry : angle 0.55694 ( 4648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.371 Fit side-chains REVERT: A 44 GLU cc_start: 0.8117 (tp30) cc_final: 0.7861 (tp30) outliers start: 13 outliers final: 8 residues processed: 83 average time/residue: 0.1226 time to fit residues: 13.1015 Evaluate side-chains 78 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 27 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.153665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126444 restraints weight = 5271.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130149 restraints weight = 2926.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132655 restraints weight = 2075.338| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3420 Z= 0.139 Angle : 0.546 7.128 4648 Z= 0.269 Chirality : 0.039 0.143 544 Planarity : 0.003 0.033 567 Dihedral : 3.879 32.141 459 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.32 % Allowed : 35.73 % Favored : 59.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.43), residues: 424 helix: 2.70 (0.29), residues: 325 sheet: -2.43 (1.52), residues: 10 loop : -0.83 (0.73), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.009 0.001 PHE A 194 TYR 0.012 0.001 TYR A 444 ARG 0.000 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 258) hydrogen bonds : angle 3.87689 ( 762) covalent geometry : bond 0.00308 ( 3420) covalent geometry : angle 0.54645 ( 4648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.334 Fit side-chains REVERT: A 192 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7271 (ttp80) outliers start: 15 outliers final: 9 residues processed: 84 average time/residue: 0.1394 time to fit residues: 14.7595 Evaluate side-chains 84 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 14 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.153174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125820 restraints weight = 5341.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.129527 restraints weight = 2951.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131561 restraints weight = 2093.813| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3420 Z= 0.146 Angle : 0.572 7.046 4648 Z= 0.281 Chirality : 0.039 0.159 544 Planarity : 0.003 0.034 567 Dihedral : 3.933 33.676 459 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.90 % Allowed : 37.46 % Favored : 57.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.43), residues: 424 helix: 2.67 (0.29), residues: 326 sheet: -2.73 (1.42), residues: 10 loop : -0.72 (0.74), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.003 0.001 HIS A 348 PHE 0.015 0.001 PHE A 417 TYR 0.012 0.001 TYR A 444 ARG 0.001 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 258) hydrogen bonds : angle 3.86460 ( 762) covalent geometry : bond 0.00325 ( 3420) covalent geometry : angle 0.57160 ( 4648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.352 Fit side-chains REVERT: A 117 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7785 (mpp) outliers start: 17 outliers final: 11 residues processed: 81 average time/residue: 0.1111 time to fit residues: 11.6349 Evaluate side-chains 83 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 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 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.154524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.127299 restraints weight = 5420.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131174 restraints weight = 2958.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.133675 restraints weight = 2068.872| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3420 Z= 0.131 Angle : 0.585 7.374 4648 Z= 0.281 Chirality : 0.040 0.189 544 Planarity : 0.003 0.034 567 Dihedral : 3.931 33.594 459 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.90 % Allowed : 37.75 % Favored : 57.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.43), residues: 424 helix: 2.70 (0.29), residues: 326 sheet: -2.71 (1.43), residues: 10 loop : -0.71 (0.74), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.003 0.000 HIS A 348 PHE 0.009 0.001 PHE A 240 TYR 0.012 0.001 TYR A 444 ARG 0.000 0.000 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 258) hydrogen bonds : angle 3.83859 ( 762) covalent geometry : bond 0.00280 ( 3420) covalent geometry : angle 0.58522 ( 4648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.345 Fit side-chains REVERT: A 117 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7792 (mpp) REVERT: A 192 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7246 (ttp80) REVERT: A 311 LYS cc_start: 0.6030 (OUTLIER) cc_final: 0.5465 (pttp) outliers start: 17 outliers final: 12 residues processed: 85 average time/residue: 0.1331 time to fit residues: 14.2412 Evaluate side-chains 85 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.151324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124180 restraints weight = 5393.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.127904 restraints weight = 2974.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.130256 restraints weight = 2090.223| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3420 Z= 0.142 Angle : 0.587 7.453 4648 Z= 0.285 Chirality : 0.040 0.177 544 Planarity : 0.003 0.032 567 Dihedral : 3.956 34.532 459 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 6.05 % Allowed : 36.60 % Favored : 57.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.43), residues: 424 helix: 2.72 (0.29), residues: 326 sheet: -2.85 (1.40), residues: 10 loop : -0.71 (0.74), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.016 0.001 PHE A 417 TYR 0.014 0.001 TYR A 444 ARG 0.001 0.000 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 258) hydrogen bonds : angle 3.85458 ( 762) covalent geometry : bond 0.00316 ( 3420) covalent geometry : angle 0.58711 ( 4648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.364 Fit side-chains REVERT: A 117 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7755 (mpp) REVERT: A 192 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7263 (ttp80) REVERT: A 311 LYS cc_start: 0.5694 (OUTLIER) cc_final: 0.5454 (pttp) outliers start: 21 outliers final: 13 residues processed: 87 average time/residue: 0.1348 time to fit residues: 14.6133 Evaluate side-chains 86 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 443 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.153038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125919 restraints weight = 5361.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.129450 restraints weight = 2914.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.132072 restraints weight = 2060.787| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3420 Z= 0.147 Angle : 0.595 7.598 4648 Z= 0.287 Chirality : 0.040 0.169 544 Planarity : 0.003 0.030 567 Dihedral : 3.986 34.896 459 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.76 % Allowed : 36.31 % Favored : 57.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.43), residues: 424 helix: 2.65 (0.28), residues: 326 sheet: -2.86 (1.39), residues: 10 loop : -0.71 (0.74), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 368 HIS 0.003 0.001 HIS A 348 PHE 0.010 0.001 PHE A 194 TYR 0.013 0.001 TYR A 444 ARG 0.001 0.000 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 258) hydrogen bonds : angle 3.86778 ( 762) covalent geometry : bond 0.00334 ( 3420) covalent geometry : angle 0.59522 ( 4648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.341 Fit side-chains REVERT: A 117 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7759 (mpp) REVERT: A 192 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7278 (ttp80) outliers start: 20 outliers final: 15 residues processed: 81 average time/residue: 0.1312 time to fit residues: 13.1975 Evaluate side-chains 88 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 466 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.0670 chunk 10 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.154795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127938 restraints weight = 5354.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131714 restraints weight = 2912.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.134360 restraints weight = 2036.088| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3420 Z= 0.129 Angle : 0.602 9.250 4648 Z= 0.285 Chirality : 0.039 0.168 544 Planarity : 0.003 0.031 567 Dihedral : 3.966 34.042 459 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 6.05 % Allowed : 36.02 % Favored : 57.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.43), residues: 424 helix: 2.75 (0.28), residues: 325 sheet: -2.64 (1.47), residues: 10 loop : -0.74 (0.75), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.018 0.001 PHE A 417 TYR 0.013 0.001 TYR A 444 ARG 0.001 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 258) hydrogen bonds : angle 3.76793 ( 762) covalent geometry : bond 0.00280 ( 3420) covalent geometry : angle 0.60219 ( 4648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.378 Fit side-chains REVERT: A 117 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7728 (mpp) REVERT: A 192 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7247 (ttp80) outliers start: 21 outliers final: 16 residues processed: 86 average time/residue: 0.1349 time to fit residues: 14.6844 Evaluate side-chains 89 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 466 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.154349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.127345 restraints weight = 5325.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130993 restraints weight = 2923.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133163 restraints weight = 2062.188| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3420 Z= 0.144 Angle : 0.614 7.889 4648 Z= 0.298 Chirality : 0.040 0.168 544 Planarity : 0.003 0.029 567 Dihedral : 3.982 34.758 459 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.19 % Allowed : 36.89 % Favored : 57.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.43), residues: 424 helix: 2.73 (0.29), residues: 325 sheet: -2.76 (1.43), residues: 10 loop : -0.72 (0.76), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.010 0.001 PHE A 194 TYR 0.013 0.001 TYR A 444 ARG 0.000 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 258) hydrogen bonds : angle 3.84838 ( 762) covalent geometry : bond 0.00323 ( 3420) covalent geometry : angle 0.61401 ( 4648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.383 Fit side-chains REVERT: A 117 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7726 (mpp) REVERT: A 192 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7272 (ttp80) outliers start: 18 outliers final: 16 residues processed: 80 average time/residue: 0.1404 time to fit residues: 14.1823 Evaluate side-chains 88 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 18 optimal weight: 0.2980 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.153824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.127132 restraints weight = 5298.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130672 restraints weight = 2900.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133306 restraints weight = 2054.219| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3420 Z= 0.146 Angle : 0.637 7.999 4648 Z= 0.309 Chirality : 0.040 0.174 544 Planarity : 0.003 0.027 567 Dihedral : 4.055 34.675 459 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.19 % Allowed : 37.75 % Favored : 57.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.43), residues: 424 helix: 2.73 (0.29), residues: 325 sheet: -2.73 (1.44), residues: 10 loop : -0.70 (0.75), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.009 0.001 PHE A 240 TYR 0.013 0.001 TYR A 444 ARG 0.001 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04277 ( 258) hydrogen bonds : angle 3.86772 ( 762) covalent geometry : bond 0.00325 ( 3420) covalent geometry : angle 0.63718 ( 4648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.371 Fit side-chains REVERT: A 117 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7669 (mpp) REVERT: A 192 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7259 (ttp80) outliers start: 18 outliers final: 16 residues processed: 80 average time/residue: 0.1414 time to fit residues: 14.2217 Evaluate side-chains 88 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 5 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.154231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.126997 restraints weight = 5348.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130720 restraints weight = 2964.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132723 restraints weight = 2087.605| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3420 Z= 0.149 Angle : 0.632 7.830 4648 Z= 0.309 Chirality : 0.040 0.172 544 Planarity : 0.003 0.027 567 Dihedral : 4.130 35.002 459 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.76 % Allowed : 37.75 % Favored : 56.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.43), residues: 424 helix: 2.69 (0.29), residues: 325 sheet: -2.76 (1.43), residues: 10 loop : -0.70 (0.75), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.009 0.001 PHE A 240 TYR 0.013 0.001 TYR A 444 ARG 0.001 0.000 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 258) hydrogen bonds : angle 3.88126 ( 762) covalent geometry : bond 0.00332 ( 3420) covalent geometry : angle 0.63184 ( 4648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1370.10 seconds wall clock time: 24 minutes 36.48 seconds (1476.48 seconds total)