Starting phenix.real_space_refine on Fri Feb 14 17:30:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmy_13544/02_2025/7pmy_13544.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmy_13544/02_2025/7pmy_13544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pmy_13544/02_2025/7pmy_13544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmy_13544/02_2025/7pmy_13544.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmy_13544/02_2025/7pmy_13544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmy_13544/02_2025/7pmy_13544.cif" } resolution = 3.8 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 3425 2.51 5 N 845 2.21 5 O 924 1.98 5 H 5276 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10499 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 10466 Classifications: {'peptide': 657} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 632} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Classifications: {'peptide': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 1} Time building chain proxies: 5.43, per 1000 atoms: 0.52 Number of scatterers: 10499 At special positions: 0 Unit cell: (85.85, 82.45, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 924 8.00 N 845 7.00 C 3425 6.00 H 5276 1.00 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: 3.10 Conformation dependent library (CDL) restraints added in 767.8 milliseconds 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1238 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 7 sheets defined 62.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 41 through 46 removed outlier: 4.142A pdb=" N ILE A 46 " --> pdb=" O TYR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 66 removed outlier: 3.630A pdb=" N VAL A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 74 Processing helix chain 'A' and resid 78 through 95 Processing helix chain 'A' and resid 96 through 108 removed outlier: 4.073A pdb=" N TRP A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.706A pdb=" N GLY A 137 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 171 removed outlier: 3.988A pdb=" N VAL A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Proline residue: A 162 - end of helix removed outlier: 3.627A pdb=" N ALA A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 208 Proline residue: A 203 - end of helix removed outlier: 3.828A pdb=" N GLY A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 238 removed outlier: 4.082A pdb=" N ALA A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) Proline residue: A 224 - end of helix removed outlier: 3.750A pdb=" N VAL A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 249 through 270 removed outlier: 4.671A pdb=" N ALA A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.734A pdb=" N TRP A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.629A pdb=" N VAL A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 Proline residue: A 308 - end of helix No H-bonds generated for 'chain 'A' and resid 305 through 308' Processing helix chain 'A' and resid 309 through 317 removed outlier: 3.754A pdb=" N TRP A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 328 removed outlier: 4.706A pdb=" N THR A 324 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 346 through 362 removed outlier: 3.521A pdb=" N ILE A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Proline residue: A 357 - end of helix removed outlier: 7.533A pdb=" N ASP A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 372 through 376 removed outlier: 4.149A pdb=" N SER A 376 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 405 removed outlier: 3.631A pdb=" N ALA A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 610 Processing helix chain 'A' and resid 611 through 637 removed outlier: 3.762A pdb=" N TYR A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 627 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 667 removed outlier: 3.763A pdb=" N LEU A 645 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 650 " --> pdb=" O GLN A 646 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 660 " --> pdb=" O GLY A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 695 removed outlier: 3.617A pdb=" N ILE A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 447 through 448 Processing sheet with id=AA2, first strand: chain 'A' and resid 447 through 448 Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 443 removed outlier: 3.605A pdb=" N LEU A 439 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AA5, first strand: chain 'A' and resid 544 through 545 removed outlier: 6.558A pdb=" N THR A 516 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N PHE A 583 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG A 518 " --> pdb=" O PHE A 583 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 585 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 520 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ASN A 587 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA A 580 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 537 through 539 removed outlier: 4.031A pdb=" N HIS A 560 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 555 333 hydrogen bonds defined for protein. 936 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: 4.37 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5265 1.03 - 1.23: 11 1.23 - 1.42: 2276 1.42 - 1.61: 3032 1.61 - 1.81: 47 Bond restraints: 10631 Sorted by residual: bond pdb=" N ASN A 41 " pdb=" CA ASN A 41 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N ASN A 41 " pdb=" H ASN A 41 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" CA VAL A 430 " pdb=" CB VAL A 430 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 1.02e+00 bond pdb=" CA HIS A 176 " pdb=" C HIS A 176 " ideal model delta sigma weight residual 1.531 1.522 0.009 1.12e-02 7.97e+03 7.14e-01 bond pdb=" CA ILE A 307 " pdb=" CB ILE A 307 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.08e-01 ... (remaining 10626 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 17586 0.92 - 1.84: 1551 1.84 - 2.76: 57 2.76 - 3.69: 16 3.69 - 4.61: 11 Bond angle restraints: 19221 Sorted by residual: angle pdb=" N ILE A 354 " pdb=" CA ILE A 354 " pdb=" C ILE A 354 " ideal model delta sigma weight residual 112.96 109.35 3.61 1.00e+00 1.00e+00 1.31e+01 angle pdb=" N HIS A 524 " pdb=" CA HIS A 524 " pdb=" C HIS A 524 " ideal model delta sigma weight residual 112.93 110.07 2.86 1.12e+00 7.97e-01 6.54e+00 angle pdb=" N SER A 640 " pdb=" CA SER A 640 " pdb=" CB SER A 640 " ideal model delta sigma weight residual 113.65 110.20 3.45 1.47e+00 4.63e-01 5.51e+00 angle pdb=" N ARG A 509 " pdb=" CA ARG A 509 " pdb=" C ARG A 509 " ideal model delta sigma weight residual 114.56 111.70 2.86 1.27e+00 6.20e-01 5.06e+00 angle pdb=" C PHE A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta sigma weight residual 122.97 120.99 1.98 9.80e-01 1.04e+00 4.10e+00 ... (remaining 19216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 4663 15.36 - 30.72: 212 30.72 - 46.09: 73 46.09 - 61.45: 63 61.45 - 76.81: 4 Dihedral angle restraints: 5015 sinusoidal: 2646 harmonic: 2369 Sorted by residual: dihedral pdb=" CA LYS A 244 " pdb=" CB LYS A 244 " pdb=" CG LYS A 244 " pdb=" CD LYS A 244 " ideal model delta sinusoidal sigma weight residual 180.00 -120.50 -59.50 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LEU A 309 " pdb=" C LEU A 309 " pdb=" N PRO A 310 " pdb=" CA PRO A 310 " ideal model delta harmonic sigma weight residual -180.00 -164.71 -15.29 0 5.00e+00 4.00e-02 9.35e+00 dihedral pdb=" N HIS A 125 " pdb=" CA HIS A 125 " pdb=" CB HIS A 125 " pdb=" CG HIS A 125 " ideal model delta sinusoidal sigma weight residual -180.00 -127.17 -52.83 3 1.50e+01 4.44e-03 9.15e+00 ... (remaining 5012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 578 0.029 - 0.058: 159 0.058 - 0.088: 59 0.088 - 0.117: 32 0.117 - 0.146: 4 Chirality restraints: 832 Sorted by residual: chirality pdb=" CA ILE A 356 " pdb=" N ILE A 356 " pdb=" C ILE A 356 " pdb=" CB ILE A 356 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE A 598 " pdb=" N ILE A 598 " pdb=" C ILE A 598 " pdb=" CB ILE A 598 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA ILE A 601 " pdb=" N ILE A 601 " pdb=" C ILE A 601 " pdb=" CB ILE A 601 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 829 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 601 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO A 602 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 602 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 602 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 307 " 0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 308 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 309 " -0.016 5.00e-02 4.00e+02 2.37e-02 8.95e-01 pdb=" N PRO A 310 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " -0.013 5.00e-02 4.00e+02 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 885 2.23 - 2.82: 23188 2.82 - 3.41: 28626 3.41 - 4.01: 37576 4.01 - 4.60: 57865 Nonbonded interactions: 148140 Sorted by model distance: nonbonded pdb=" OE2 GLU A 507 " pdb=" H THR A 510 " model vdw 1.631 2.450 nonbonded pdb=" H GLN A 412 " pdb=" OE1 GLU A 483 " model vdw 1.640 2.450 nonbonded pdb=" HE ARG A 266 " pdb=" OE1 GLN A 278 " model vdw 1.654 2.450 nonbonded pdb=" OD2 ASP A 317 " pdb="HD22 ASN A 657 " model vdw 1.655 2.450 nonbonded pdb="HH22 ARG A 277 " pdb=" OE2 GLU A 286 " model vdw 1.659 2.450 ... (remaining 148135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.160 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.690 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 0.002 0.033 5355 Z= 0.147 Angle : 0.460 4.606 7278 Z= 0.276 Chirality : 0.036 0.146 832 Planarity : 0.003 0.031 906 Dihedral : 9.150 67.769 1896 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.98 % Favored : 97.86 % Rotamer: Outliers : 1.40 % Allowed : 3.51 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.55 (0.33), residues: 655 helix: 0.76 (0.29), residues: 336 sheet: 0.40 (0.51), residues: 104 loop : -0.08 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 313 HIS 0.001 0.000 HIS A 467 PHE 0.007 0.001 PHE A 172 TYR 0.010 0.001 TYR A 121 ARG 0.002 0.000 ARG A 562 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9282 (tp) cc_final: 0.8998 (tt) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.3890 time to fit residues: 45.2534 Evaluate side-chains 67 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 618 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 ASN A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.133554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.098749 restraints weight = 31496.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.096479 restraints weight = 29978.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.098528 restraints weight = 28060.216| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5355 Z= 0.282 Angle : 0.592 5.000 7278 Z= 0.332 Chirality : 0.041 0.138 832 Planarity : 0.005 0.065 906 Dihedral : 6.107 58.324 718 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.90 % Favored : 96.79 % Rotamer: Outliers : 1.75 % Allowed : 7.54 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.30 (0.32), residues: 655 helix: 0.89 (0.27), residues: 352 sheet: 0.01 (0.52), residues: 93 loop : -0.74 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 596 HIS 0.002 0.001 HIS A 467 PHE 0.014 0.002 PHE A 261 TYR 0.024 0.001 TYR A 121 ARG 0.005 0.001 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9123 (tp) cc_final: 0.8829 (tt) outliers start: 10 outliers final: 9 residues processed: 74 average time/residue: 0.3597 time to fit residues: 35.3492 Evaluate side-chains 63 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 618 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 50 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 62 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.134443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.099727 restraints weight = 32008.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099028 restraints weight = 34990.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.101231 restraints weight = 29377.968| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5355 Z= 0.195 Angle : 0.520 4.869 7278 Z= 0.285 Chirality : 0.039 0.139 832 Planarity : 0.004 0.054 906 Dihedral : 6.034 59.129 718 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.93 % Allowed : 8.07 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.36 (0.32), residues: 655 helix: 1.19 (0.27), residues: 341 sheet: -0.05 (0.51), residues: 93 loop : -1.07 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 596 HIS 0.002 0.001 HIS A 87 PHE 0.017 0.001 PHE A 261 TYR 0.018 0.001 TYR A 121 ARG 0.004 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9091 (tp) cc_final: 0.8795 (tt) outliers start: 11 outliers final: 10 residues processed: 67 average time/residue: 0.3789 time to fit residues: 33.5287 Evaluate side-chains 65 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.134698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.099494 restraints weight = 31382.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098117 restraints weight = 27480.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.101212 restraints weight = 24199.418| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5355 Z= 0.190 Angle : 0.501 6.008 7278 Z= 0.272 Chirality : 0.039 0.137 832 Planarity : 0.004 0.049 906 Dihedral : 5.960 59.155 718 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.11 % Allowed : 8.77 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.40 (0.32), residues: 655 helix: 1.25 (0.28), residues: 342 sheet: -0.16 (0.50), residues: 93 loop : -1.07 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 596 HIS 0.003 0.001 HIS A 87 PHE 0.017 0.001 PHE A 261 TYR 0.020 0.001 TYR A 121 ARG 0.001 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9147 (tp) cc_final: 0.8844 (tt) outliers start: 12 outliers final: 9 residues processed: 68 average time/residue: 0.3777 time to fit residues: 33.9716 Evaluate side-chains 63 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 46 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.140591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.105580 restraints weight = 33544.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.106527 restraints weight = 29448.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.107575 restraints weight = 25244.674| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5355 Z= 0.205 Angle : 0.495 5.967 7278 Z= 0.269 Chirality : 0.038 0.140 832 Planarity : 0.004 0.046 906 Dihedral : 5.819 59.067 717 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.58 % Allowed : 10.00 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.47 (0.32), residues: 655 helix: 1.31 (0.28), residues: 345 sheet: -0.38 (0.49), residues: 100 loop : -0.92 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 596 HIS 0.003 0.001 HIS A 87 PHE 0.016 0.001 PHE A 261 TYR 0.022 0.001 TYR A 121 ARG 0.003 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9317 (tp) cc_final: 0.9040 (tt) outliers start: 9 outliers final: 9 residues processed: 65 average time/residue: 0.3753 time to fit residues: 32.3212 Evaluate side-chains 62 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.139335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.101955 restraints weight = 32717.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.101699 restraints weight = 20959.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.103173 restraints weight = 16436.675| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5355 Z= 0.214 Angle : 0.507 6.659 7278 Z= 0.273 Chirality : 0.038 0.147 832 Planarity : 0.004 0.045 906 Dihedral : 5.802 58.939 717 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.75 % Allowed : 10.35 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.40 (0.32), residues: 655 helix: 1.29 (0.28), residues: 342 sheet: -0.42 (0.48), residues: 100 loop : -1.00 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 596 HIS 0.002 0.000 HIS A 87 PHE 0.016 0.001 PHE A 261 TYR 0.021 0.001 TYR A 121 ARG 0.003 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7883 (tpp-160) REVERT: A 582 LEU cc_start: 0.9386 (tp) cc_final: 0.9135 (tt) outliers start: 10 outliers final: 9 residues processed: 60 average time/residue: 0.3340 time to fit residues: 27.0151 Evaluate side-chains 62 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 39 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 0.0770 overall best weight: 1.0742 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.140400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.104000 restraints weight = 34076.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.104747 restraints weight = 22842.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.106108 restraints weight = 20104.180| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5355 Z= 0.186 Angle : 0.499 6.545 7278 Z= 0.267 Chirality : 0.038 0.144 832 Planarity : 0.004 0.043 906 Dihedral : 5.776 59.183 717 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.93 % Allowed : 9.82 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.51 (0.32), residues: 655 helix: 1.36 (0.28), residues: 342 sheet: -0.23 (0.49), residues: 100 loop : -0.98 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 596 HIS 0.003 0.000 HIS A 87 PHE 0.016 0.001 PHE A 261 TYR 0.019 0.001 TYR A 121 ARG 0.002 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7868 (tpp-160) REVERT: A 582 LEU cc_start: 0.9341 (tp) cc_final: 0.9080 (tt) outliers start: 11 outliers final: 10 residues processed: 59 average time/residue: 0.3509 time to fit residues: 28.1598 Evaluate side-chains 62 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.140427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.103977 restraints weight = 33867.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.104188 restraints weight = 23107.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.105442 restraints weight = 21757.879| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5355 Z= 0.203 Angle : 0.493 5.921 7278 Z= 0.265 Chirality : 0.038 0.148 832 Planarity : 0.004 0.043 906 Dihedral : 5.748 59.113 717 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.93 % Allowed : 10.53 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.62 (0.32), residues: 655 helix: 1.38 (0.28), residues: 344 sheet: 0.02 (0.47), residues: 106 loop : -0.96 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 596 HIS 0.003 0.001 HIS A 87 PHE 0.016 0.001 PHE A 261 TYR 0.020 0.001 TYR A 121 ARG 0.001 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7865 (tpp-160) REVERT: A 416 LEU cc_start: 0.9181 (tp) cc_final: 0.8944 (tt) REVERT: A 570 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6803 (mm) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 0.3609 time to fit residues: 28.8756 Evaluate side-chains 58 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 40 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.140185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.104236 restraints weight = 33931.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.104303 restraints weight = 24168.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.105547 restraints weight = 19759.843| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5355 Z= 0.187 Angle : 0.505 10.132 7278 Z= 0.265 Chirality : 0.038 0.142 832 Planarity : 0.004 0.043 906 Dihedral : 5.731 59.320 717 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.93 % Allowed : 11.05 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.69 (0.32), residues: 655 helix: 1.43 (0.28), residues: 344 sheet: 0.11 (0.47), residues: 106 loop : -0.96 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 596 HIS 0.003 0.000 HIS A 87 PHE 0.016 0.001 PHE A 261 TYR 0.019 0.001 TYR A 121 ARG 0.002 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7915 (tpp-160) REVERT: A 570 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6908 (mm) REVERT: A 582 LEU cc_start: 0.9357 (tp) cc_final: 0.9105 (tt) REVERT: A 692 MET cc_start: 0.8152 (ttm) cc_final: 0.7896 (ttt) outliers start: 11 outliers final: 9 residues processed: 61 average time/residue: 0.3374 time to fit residues: 27.8264 Evaluate side-chains 60 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.140467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.104549 restraints weight = 33608.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104416 restraints weight = 24245.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.106182 restraints weight = 20716.770| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5355 Z= 0.177 Angle : 0.495 9.072 7278 Z= 0.260 Chirality : 0.038 0.142 832 Planarity : 0.004 0.042 906 Dihedral : 5.699 59.384 717 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.93 % Allowed : 11.23 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.75 (0.33), residues: 655 helix: 1.49 (0.28), residues: 344 sheet: 0.15 (0.47), residues: 106 loop : -0.97 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 596 HIS 0.003 0.000 HIS A 87 PHE 0.016 0.001 PHE A 261 TYR 0.019 0.001 TYR A 121 ARG 0.003 0.000 ARG A 553 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7903 (tpp-160) REVERT: A 570 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6949 (mm) REVERT: A 692 MET cc_start: 0.8158 (ttm) cc_final: 0.7899 (ttt) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.3721 time to fit residues: 28.9788 Evaluate side-chains 59 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 27 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 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 = 0.4135 r_free = 0.4135 target = 0.141333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.105529 restraints weight = 33750.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.104657 restraints weight = 26355.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.106509 restraints weight = 22049.380| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5355 Z= 0.159 Angle : 0.492 9.748 7278 Z= 0.256 Chirality : 0.038 0.141 832 Planarity : 0.003 0.042 906 Dihedral : 5.657 59.804 717 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.93 % Allowed : 11.23 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.88 (0.33), residues: 655 helix: 1.60 (0.28), residues: 340 sheet: 0.18 (0.47), residues: 106 loop : -0.84 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 596 HIS 0.003 0.000 HIS A 87 PHE 0.016 0.001 PHE A 261 TYR 0.018 0.001 TYR A 121 ARG 0.007 0.000 ARG A 553 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3394.39 seconds wall clock time: 60 minutes 45.08 seconds (3645.08 seconds total)