Starting phenix.real_space_refine on Fri Aug 22 13:33:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p6a_17462/08_2025/8p6a_17462.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p6a_17462/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8p6a_17462/08_2025/8p6a_17462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p6a_17462/08_2025/8p6a_17462.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p6a_17462/08_2025/8p6a_17462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p6a_17462/08_2025/8p6a_17462.map" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.07, per 1000 atoms: 0.32 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: 0.22 Conformation dependent library (CDL) restraints added in 132.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.11 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: 0.53 Time building geometry restraints manager: 0.32 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: 1.750 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.360 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.410 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.001 0.000 ARG A 350 TYR 0.013 0.001 TYR A 444 PHE 0.013 0.001 PHE A 247 TRP 0.014 0.001 TRP A 368 HIS 0.002 0.000 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3420) covalent geometry : angle 0.65646 ( 4648) hydrogen bonds : bond 0.09273 ( 258) hydrogen bonds : angle 4.28419 ( 762) *********************** 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 : 0.146 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.0626 time to fit residues: 5.8328 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 : 0.122 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.151610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.124019 restraints weight = 5453.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127722 restraints weight = 2977.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129726 restraints weight = 2101.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.131441 restraints weight = 1737.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132506 restraints weight = 1512.986| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3420 Z= 0.167 Angle : 0.581 6.889 4648 Z= 0.292 Chirality : 0.039 0.147 544 Planarity : 0.003 0.038 567 Dihedral : 3.947 31.337 459 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.75 % Allowed : 35.73 % Favored : 60.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.75 (0.43), residues: 424 helix: 2.62 (0.29), residues: 325 sheet: -2.46 (1.52), residues: 10 loop : -0.77 (0.72), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 404 TYR 0.013 0.001 TYR A 444 PHE 0.011 0.001 PHE A 247 TRP 0.009 0.001 TRP A 368 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3420) covalent geometry : angle 0.58089 ( 4648) hydrogen bonds : bond 0.04529 ( 258) hydrogen bonds : angle 4.04010 ( 762) *********************** 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 90 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.130 Fit side-chains REVERT: A 44 GLU cc_start: 0.8221 (tp30) cc_final: 0.7909 (tp30) outliers start: 13 outliers final: 8 residues processed: 84 average time/residue: 0.0487 time to fit residues: 5.3147 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 : 0.102 ------------------------------------------------------------------------------- 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 5 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 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 = 0.3888 r_free = 0.3888 target = 0.152271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125159 restraints weight = 5385.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.128875 restraints weight = 2956.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131273 restraints weight = 2083.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132899 restraints weight = 1692.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.133609 restraints weight = 1482.186| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3420 Z= 0.147 Angle : 0.559 6.970 4648 Z= 0.277 Chirality : 0.039 0.144 544 Planarity : 0.003 0.036 567 Dihedral : 3.964 32.918 459 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.19 % Allowed : 36.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.78 (0.43), residues: 424 helix: 2.65 (0.29), residues: 325 sheet: -2.59 (1.46), residues: 10 loop : -0.80 (0.73), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 404 TYR 0.012 0.001 TYR A 444 PHE 0.010 0.001 PHE A 194 TRP 0.009 0.001 TRP A 368 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 3420) covalent geometry : angle 0.55895 ( 4648) hydrogen bonds : bond 0.04404 ( 258) hydrogen bonds : angle 3.94219 ( 762) *********************** 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 93 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.122 Fit side-chains REVERT: A 192 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7279 (ttp80) REVERT: A 311 LYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5344 (pttp) outliers start: 18 outliers final: 10 residues processed: 84 average time/residue: 0.0624 time to fit residues: 6.5449 Evaluate side-chains 85 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 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 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 24 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 13 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 = 0.3885 r_free = 0.3885 target = 0.152050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.124645 restraints weight = 5314.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.128307 restraints weight = 2949.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130623 restraints weight = 2098.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131537 restraints weight = 1721.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131537 restraints weight = 1559.053| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3420 Z= 0.142 Angle : 0.576 7.044 4648 Z= 0.281 Chirality : 0.039 0.152 544 Planarity : 0.003 0.037 567 Dihedral : 3.983 33.550 459 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.97 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.43), residues: 424 helix: 2.67 (0.29), residues: 325 sheet: -2.80 (1.39), residues: 10 loop : -0.78 (0.73), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 404 TYR 0.013 0.001 TYR A 444 PHE 0.010 0.001 PHE A 194 TRP 0.009 0.001 TRP A 368 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3420) covalent geometry : angle 0.57582 ( 4648) hydrogen bonds : bond 0.04345 ( 258) hydrogen bonds : angle 3.90088 ( 762) *********************** 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 90 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.139 Fit side-chains REVERT: A 117 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7819 (mpp) REVERT: A 192 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7262 (ttp80) outliers start: 21 outliers final: 12 residues processed: 81 average time/residue: 0.0628 time to fit residues: 6.4392 Evaluate side-chains 86 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 381 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.147756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.120691 restraints weight = 5406.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124221 restraints weight = 2989.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.126356 restraints weight = 2116.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.127997 restraints weight = 1734.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128608 restraints weight = 1521.782| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3420 Z= 0.211 Angle : 0.628 6.724 4648 Z= 0.314 Chirality : 0.041 0.164 544 Planarity : 0.004 0.037 567 Dihedral : 4.158 36.435 459 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 6.34 % Allowed : 37.46 % Favored : 56.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.42), residues: 424 helix: 2.42 (0.28), residues: 326 sheet: -3.47 (1.18), residues: 10 loop : -0.81 (0.73), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 404 TYR 0.011 0.001 TYR A 444 PHE 0.016 0.001 PHE A 417 TRP 0.010 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 3420) covalent geometry : angle 0.62815 ( 4648) hydrogen bonds : bond 0.04814 ( 258) hydrogen bonds : angle 4.15786 ( 762) *********************** 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: 22 poor density : 72 time to evaluate : 0.133 Fit side-chains REVERT: A 117 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7779 (mpp) REVERT: A 257 PHE cc_start: 0.6388 (OUTLIER) cc_final: 0.5411 (p90) outliers start: 22 outliers final: 15 residues processed: 85 average time/residue: 0.0471 time to fit residues: 5.2114 Evaluate side-chains 86 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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 110 LEU 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 257 PHE 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 429 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 466 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 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 = 0.3878 r_free = 0.3878 target = 0.151426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124382 restraints weight = 5346.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.128002 restraints weight = 2940.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130310 restraints weight = 2083.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131946 restraints weight = 1698.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.132348 restraints weight = 1487.358| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1146 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= 0.152 Angle : 0.610 7.445 4648 Z= 0.298 Chirality : 0.040 0.167 544 Planarity : 0.003 0.039 567 Dihedral : 4.130 35.119 459 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 6.05 % Allowed : 37.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.43), residues: 424 helix: 2.61 (0.29), residues: 325 sheet: -3.49 (1.18), residues: 10 loop : -0.82 (0.73), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 393 TYR 0.013 0.001 TYR A 444 PHE 0.012 0.001 PHE A 240 TRP 0.011 0.001 TRP A 368 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3420) covalent geometry : angle 0.60977 ( 4648) hydrogen bonds : bond 0.04519 ( 258) hydrogen bonds : angle 3.95974 ( 762) *********************** 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 : 0.133 Fit side-chains REVERT: A 117 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7808 (mpp) REVERT: A 192 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7277 (ttp80) outliers start: 21 outliers final: 16 residues processed: 86 average time/residue: 0.0584 time to fit residues: 6.3727 Evaluate side-chains 86 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 110 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 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 449 LEU 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 41 optimal weight: 0.6980 chunk 3 optimal weight: 0.0030 chunk 10 optimal weight: 0.0770 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.4348 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.153473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126918 restraints weight = 5447.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.130694 restraints weight = 2914.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.132629 restraints weight = 2023.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.134484 restraints weight = 1664.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.135498 restraints weight = 1447.517| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1215 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= 0.133 Angle : 0.612 8.304 4648 Z= 0.292 Chirality : 0.039 0.171 544 Planarity : 0.003 0.033 567 Dihedral : 4.065 34.727 459 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.76 % Allowed : 38.04 % Favored : 56.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.43), residues: 424 helix: 2.74 (0.28), residues: 325 sheet: -3.29 (1.24), residues: 10 loop : -0.74 (0.73), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 394 TYR 0.017 0.001 TYR A 342 PHE 0.010 0.001 PHE A 240 TRP 0.013 0.001 TRP A 368 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3420) covalent geometry : angle 0.61241 ( 4648) hydrogen bonds : bond 0.04250 ( 258) hydrogen bonds : angle 3.82716 ( 762) *********************** 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 92 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.144 Fit side-chains REVERT: A 117 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7732 (mpp) REVERT: A 192 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7226 (ttp80) outliers start: 20 outliers final: 14 residues processed: 84 average time/residue: 0.0588 time to fit residues: 6.3182 Evaluate side-chains 85 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU 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 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 449 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 34 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 chunk 10 optimal weight: 0.1980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.154840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.127787 restraints weight = 5402.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.131498 restraints weight = 2913.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133770 restraints weight = 2044.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135549 restraints weight = 1662.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.136664 restraints weight = 1435.489| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1191 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= 0.133 Angle : 0.607 8.086 4648 Z= 0.290 Chirality : 0.040 0.166 544 Planarity : 0.003 0.028 567 Dihedral : 4.027 34.347 459 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.61 % Allowed : 38.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.85 (0.43), residues: 424 helix: 2.71 (0.28), residues: 325 sheet: -3.21 (1.27), residues: 10 loop : -0.70 (0.74), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 394 TYR 0.014 0.001 TYR A 444 PHE 0.010 0.001 PHE A 240 TRP 0.013 0.001 TRP A 368 HIS 0.003 0.000 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3420) covalent geometry : angle 0.60658 ( 4648) hydrogen bonds : bond 0.04259 ( 258) hydrogen bonds : angle 3.81130 ( 762) *********************** 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 88 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.140 Fit side-chains REVERT: A 117 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7713 (mpp) REVERT: A 192 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7271 (ttp80) outliers start: 16 outliers final: 12 residues processed: 81 average time/residue: 0.0585 time to fit residues: 5.9941 Evaluate side-chains 84 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU 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 329 ILE Chi-restraints excluded: chain A residue 333 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 0.0070 chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.154537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.127583 restraints weight = 5349.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131370 restraints weight = 2941.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133598 restraints weight = 2062.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135242 restraints weight = 1681.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135242 restraints weight = 1448.624| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1306 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= 0.141 Angle : 0.628 7.759 4648 Z= 0.303 Chirality : 0.040 0.170 544 Planarity : 0.003 0.029 567 Dihedral : 4.036 34.731 459 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.76 % Allowed : 38.33 % Favored : 55.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.43), residues: 424 helix: 2.71 (0.28), residues: 325 sheet: -3.15 (1.31), residues: 10 loop : -0.68 (0.75), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 394 TYR 0.014 0.001 TYR A 444 PHE 0.009 0.001 PHE A 240 TRP 0.013 0.001 TRP A 368 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 3420) covalent geometry : angle 0.62822 ( 4648) hydrogen bonds : bond 0.04272 ( 258) hydrogen bonds : angle 3.83492 ( 762) *********************** 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 90 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.154 Fit side-chains REVERT: A 117 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7706 (mpp) REVERT: A 192 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7292 (ttp80) outliers start: 20 outliers final: 16 residues processed: 81 average time/residue: 0.0596 time to fit residues: 6.1516 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 : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 110 LEU 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 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 449 LEU 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 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.153978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126784 restraints weight = 5288.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.130513 restraints weight = 2925.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132767 restraints weight = 2061.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.134452 restraints weight = 1684.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.135356 restraints weight = 1483.646| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1278 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= 0.150 Angle : 0.640 8.886 4648 Z= 0.312 Chirality : 0.040 0.170 544 Planarity : 0.003 0.028 567 Dihedral : 4.179 35.033 459 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.19 % Allowed : 38.62 % Favored : 56.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.43), residues: 424 helix: 2.65 (0.28), residues: 325 sheet: -3.20 (1.29), residues: 10 loop : -0.65 (0.75), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 394 TYR 0.014 0.001 TYR A 444 PHE 0.010 0.001 PHE A 240 TRP 0.013 0.001 TRP A 368 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3420) covalent geometry : angle 0.64049 ( 4648) hydrogen bonds : bond 0.04491 ( 258) hydrogen bonds : angle 3.89185 ( 762) ********************** 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 88 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.127 Fit side-chains REVERT: A 117 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7701 (mpp) REVERT: A 192 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7303 (ttp80) outliers start: 18 outliers final: 16 residues processed: 79 average time/residue: 0.0610 time to fit residues: 6.1103 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 : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 110 LEU 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 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 449 LEU 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 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 25 optimal weight: 0.0970 chunk 12 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.153989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128858 restraints weight = 5321.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.132586 restraints weight = 2788.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.135171 restraints weight = 1899.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.136262 restraints weight = 1497.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.137173 restraints weight = 1326.931| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1374 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= 0.140 Angle : 0.641 8.730 4648 Z= 0.311 Chirality : 0.040 0.173 544 Planarity : 0.003 0.028 567 Dihedral : 4.132 34.527 459 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.19 % Allowed : 38.90 % Favored : 55.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.43), residues: 424 helix: 2.71 (0.28), residues: 325 sheet: -3.07 (1.33), residues: 10 loop : -0.64 (0.75), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 394 TYR 0.014 0.001 TYR A 444 PHE 0.010 0.001 PHE A 240 TRP 0.014 0.001 TRP A 368 HIS 0.002 0.000 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3420) covalent geometry : angle 0.64139 ( 4648) hydrogen bonds : bond 0.04360 ( 258) hydrogen bonds : angle 3.80766 ( 762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 806.84 seconds wall clock time: 14 minutes 37.15 seconds (877.15 seconds total)