Starting phenix.real_space_refine on Sat Apr 26 20:31:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p6a_17462/04_2025/8p6a_17462.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p6a_17462/04_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_17462/04_2025/8p6a_17462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p6a_17462/04_2025/8p6a_17462.map" model { file = "/net/cci-nas-00/data/ceres_data/8p6a_17462/04_2025/8p6a_17462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p6a_17462/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 3.73, per 1000 atoms: 1.12 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 694.8 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: 0.39 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: 0.89 Time building geometry restraints manager: 0.98 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: 2.030 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 14.630 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.010 ------------------------------------------------------------------------------- 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 : 0.380 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.1424 time to fit residues: 13.2172 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 : 0.384 ------------------------------------------------------------------------------- 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: 0.0470 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: 0.2894 ------------------------------------------------------------------------------- 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 = 0.155518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128701 restraints weight = 5330.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132520 restraints weight = 2870.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134612 restraints weight = 2003.603| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3420 Z= 0.124 Angle : 0.555 7.273 4648 Z= 0.273 Chirality : 0.038 0.150 544 Planarity : 0.003 0.036 567 Dihedral : 3.853 28.912 459 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.75 % Allowed : 34.87 % Favored : 61.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.71 (0.28), residues: 325 sheet: -2.22 (1.61), residues: 10 loop : -0.75 (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 0.04158 ( 258) hydrogen bonds : angle 3.88454 ( 762) covalent geometry : bond 0.00248 ( 3420) covalent geometry : angle 0.55465 ( 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 : 0.357 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 83 average time/residue: 0.1338 time to fit residues: 14.4308 Evaluate side-chains 77 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 18 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 0.0470 chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.155855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128423 restraints weight = 5255.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.132188 restraints weight = 2912.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134397 restraints weight = 2063.860| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3420 Z= 0.125 Angle : 0.530 7.295 4648 Z= 0.261 Chirality : 0.038 0.143 544 Planarity : 0.003 0.034 567 Dihedral : 3.829 30.914 459 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.75 % Allowed : 35.45 % Favored : 60.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.87 (0.43), residues: 424 helix: 2.73 (0.28), residues: 325 sheet: -2.27 (1.59), residues: 10 loop : -0.87 (0.72), 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 0.008 0.001 PHE A 194 TYR 0.012 0.001 TYR A 444 ARG 0.000 0.000 ARG A 104 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 258) hydrogen bonds : angle 3.83177 ( 762) covalent geometry : bond 0.00265 ( 3420) covalent geometry : angle 0.52994 ( 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 92 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.345 Fit side-chains REVERT: A 95 LEU cc_start: 0.8860 (tp) cc_final: 0.8653 (tt) REVERT: A 117 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7902 (mpp) REVERT: A 192 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7245 (ttp80) outliers start: 13 outliers final: 9 residues processed: 86 average time/residue: 0.1297 time to fit residues: 14.0193 Evaluate side-chains 88 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.153933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.126569 restraints weight = 5340.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130303 restraints weight = 2959.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132821 restraints weight = 2089.714| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3420 Z= 0.147 Angle : 0.551 7.047 4648 Z= 0.276 Chirality : 0.039 0.155 544 Planarity : 0.003 0.033 567 Dihedral : 3.898 33.545 459 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.48 % Allowed : 36.31 % Favored : 58.21 % 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: 2.72 (0.28), residues: 325 sheet: -2.51 (1.50), residues: 10 loop : -0.76 (0.73), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.002 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 0.04186 ( 258) hydrogen bonds : angle 3.85695 ( 762) covalent geometry : bond 0.00331 ( 3420) covalent geometry : angle 0.55102 ( 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 96 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.385 Fit side-chains REVERT: A 44 GLU cc_start: 0.8180 (tp30) cc_final: 0.7866 (tp30) REVERT: A 95 LEU cc_start: 0.8849 (tp) cc_final: 0.8633 (tt) REVERT: A 117 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7840 (mmp) REVERT: A 192 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7287 (ttp80) outliers start: 19 outliers final: 10 residues processed: 87 average time/residue: 0.1359 time to fit residues: 14.8620 Evaluate side-chains 86 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 329 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 346 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.154476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.127302 restraints weight = 5417.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131094 restraints weight = 2952.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.133259 restraints weight = 2070.545| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 0.031 3420 Z= 0.133 Angle : 0.568 7.349 4648 Z= 0.278 Chirality : 0.040 0.193 544 Planarity : 0.003 0.033 567 Dihedral : 3.918 33.508 459 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: 2.89 (0.43), residues: 424 helix: 2.73 (0.28), residues: 325 sheet: -2.56 (1.49), residues: 10 loop : -0.74 (0.74), residues: 89 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 404 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 258) hydrogen bonds : angle 3.83847 ( 762) covalent geometry : bond 0.00292 ( 3420) covalent geometry : angle 0.56828 ( 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 94 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.395 Fit side-chains REVERT: A 95 LEU cc_start: 0.8849 (tp) cc_final: 0.8640 (tt) REVERT: A 117 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7810 (mpp) REVERT: A 192 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7254 (ttp80) REVERT: A 311 LYS cc_start: 0.6010 (OUTLIER) cc_final: 0.5420 (pttp) outliers start: 18 outliers final: 12 residues processed: 86 average time/residue: 0.1410 time to fit residues: 15.3159 Evaluate side-chains 87 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 338 MET 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: 0.5980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 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 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.153255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125695 restraints weight = 5466.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.129463 restraints weight = 3022.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131665 restraints weight = 2135.153| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1041 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= 0.142 Angle : 0.571 7.356 4648 Z= 0.281 Chirality : 0.039 0.170 544 Planarity : 0.003 0.032 567 Dihedral : 3.946 34.475 459 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 6.05 % Allowed : 36.31 % 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: 2.87 (0.43), residues: 424 helix: 2.71 (0.28), residues: 325 sheet: -2.64 (1.46), residues: 10 loop : -0.73 (0.74), residues: 89 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 0.013 0.001 TYR A 444 ARG 0.001 0.000 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 258) hydrogen bonds : angle 3.85836 ( 762) covalent geometry : bond 0.00317 ( 3420) covalent geometry : angle 0.57091 ( 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 93 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.358 Fit side-chains REVERT: A 95 LEU cc_start: 0.8847 (tp) cc_final: 0.8640 (tt) REVERT: A 117 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7950 (mpp) REVERT: A 192 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7258 (ttp80) outliers start: 21 outliers final: 15 residues processed: 83 average time/residue: 0.1349 time to fit residues: 13.9580 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 : 0.357 ------------------------------------------------------------------------------- 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 223 VAL 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 338 MET Chi-restraints excluded: chain A residue 346 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 0 optimal weight: 0.5980 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 = 0.3901 r_free = 0.3901 target = 0.153158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126016 restraints weight = 5397.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129751 restraints weight = 2963.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.131997 restraints weight = 2087.857| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3420 Z= 0.144 Angle : 0.584 7.612 4648 Z= 0.285 Chirality : 0.039 0.172 544 Planarity : 0.003 0.029 567 Dihedral : 3.958 34.831 459 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.76 % Allowed : 36.60 % 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: 2.69 (0.28), residues: 325 sheet: -2.74 (1.43), residues: 10 loop : -0.77 (0.74), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.010 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 0.04247 ( 258) hydrogen bonds : angle 3.83860 ( 762) covalent geometry : bond 0.00327 ( 3420) covalent geometry : angle 0.58360 ( 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 90 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.346 Fit side-chains REVERT: A 95 LEU cc_start: 0.8861 (tp) cc_final: 0.8647 (tt) REVERT: A 117 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7922 (mmp) REVERT: A 192 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7269 (ttp80) outliers start: 20 outliers final: 16 residues processed: 80 average time/residue: 0.1350 time to fit residues: 13.5312 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 : 0.386 ------------------------------------------------------------------------------- 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 223 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.0570 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.153837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127090 restraints weight = 5342.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130789 restraints weight = 2911.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.133038 restraints weight = 2040.650| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1156 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= 0.135 Angle : 0.584 8.649 4648 Z= 0.281 Chirality : 0.039 0.171 544 Planarity : 0.003 0.029 567 Dihedral : 3.949 34.688 459 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 6.34 % Allowed : 35.73 % 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: 2.87 (0.43), residues: 424 helix: 2.71 (0.28), residues: 325 sheet: -2.74 (1.44), residues: 10 loop : -0.75 (0.75), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 368 HIS 0.002 0.000 HIS A 348 PHE 0.017 0.001 PHE A 417 TYR 0.013 0.001 TYR A 444 ARG 0.001 0.000 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 258) hydrogen bonds : angle 3.81273 ( 762) covalent geometry : bond 0.00298 ( 3420) covalent geometry : angle 0.58403 ( 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 94 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.356 Fit side-chains REVERT: A 95 LEU cc_start: 0.8859 (tp) cc_final: 0.8646 (tt) REVERT: A 117 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7964 (mpp) REVERT: A 192 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7262 (ttp80) outliers start: 22 outliers final: 16 residues processed: 85 average time/residue: 0.1298 time to fit residues: 13.8933 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 : 0.436 ------------------------------------------------------------------------------- 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 223 VAL 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 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: 0.6980 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.152547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125569 restraints weight = 5376.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129302 restraints weight = 2953.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131459 restraints weight = 2070.544| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3420 Z= 0.159 Angle : 0.613 7.708 4648 Z= 0.300 Chirality : 0.040 0.163 544 Planarity : 0.003 0.030 567 Dihedral : 4.012 35.485 459 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.48 % Allowed : 36.31 % Favored : 58.21 % 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: 2.79 (0.43), residues: 424 helix: 2.65 (0.28), residues: 325 sheet: -2.87 (1.39), residues: 10 loop : -0.75 (0.75), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.001 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 258) hydrogen bonds : angle 3.90812 ( 762) covalent geometry : bond 0.00369 ( 3420) covalent geometry : angle 0.61301 ( 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 92 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.390 Fit side-chains REVERT: A 95 LEU cc_start: 0.8879 (tp) cc_final: 0.8660 (tt) REVERT: A 117 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7968 (mpp) REVERT: A 192 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7290 (ttp80) outliers start: 19 outliers final: 16 residues processed: 83 average time/residue: 0.1395 time to fit residues: 14.6282 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 : 0.394 ------------------------------------------------------------------------------- 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 223 VAL 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 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: 4.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.152849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125605 restraints weight = 5328.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.129218 restraints weight = 2956.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131218 restraints weight = 2095.236| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3420 Z= 0.157 Angle : 0.622 7.635 4648 Z= 0.306 Chirality : 0.040 0.164 544 Planarity : 0.003 0.030 567 Dihedral : 4.080 35.529 459 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.48 % Allowed : 36.60 % 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: 2.76 (0.43), residues: 424 helix: 2.64 (0.29), residues: 325 sheet: -2.89 (1.38), residues: 10 loop : -0.76 (0.74), 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 0.016 0.001 PHE A 417 TYR 0.012 0.001 TYR A 444 ARG 0.001 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 258) hydrogen bonds : angle 3.95464 ( 762) covalent geometry : bond 0.00358 ( 3420) covalent geometry : angle 0.62229 ( 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: 19 poor density : 70 time to evaluate : 0.380 Fit side-chains REVERT: A 95 LEU cc_start: 0.8859 (tp) cc_final: 0.8652 (tt) REVERT: A 192 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7290 (ttp80) outliers start: 19 outliers final: 17 residues processed: 80 average time/residue: 0.1312 time to fit residues: 13.2191 Evaluate side-chains 87 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 175 ILE Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 223 VAL 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: 0.8980 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 0.0970 chunk 2 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.152588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125704 restraints weight = 5405.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.129399 restraints weight = 2960.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131354 restraints weight = 2081.139| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3420 Z= 0.156 Angle : 0.655 10.393 4648 Z= 0.320 Chirality : 0.040 0.167 544 Planarity : 0.003 0.030 567 Dihedral : 4.181 35.454 459 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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: 2.79 (0.43), residues: 424 helix: 2.65 (0.29), residues: 325 sheet: -2.84 (1.40), residues: 10 loop : -0.72 (0.74), 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 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 0.04566 ( 258) hydrogen bonds : angle 3.93614 ( 762) covalent geometry : bond 0.00351 ( 3420) covalent geometry : angle 0.65524 ( 4648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1463.72 seconds wall clock time: 26 minutes 15.07 seconds (1575.07 seconds total)