Starting phenix.real_space_refine on Tue Aug 4 17:44:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22ax_68140/08_2026/22ax_68140.cif Found real_map, /net/cci-nas-00/data/ceres_data/22ax_68140/08_2026/22ax_68140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22ax_68140/08_2026/22ax_68140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22ax_68140/08_2026/22ax_68140.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22ax_68140/08_2026/22ax_68140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22ax_68140/08_2026/22ax_68140.map" } resolution = 3.3 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= -0.000 sd= 0.004 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 P 39 5.49 5 S 29 5.16 5 C 3314 2.51 5 N 939 2.21 5 O 1103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5424 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4567 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 538} Chain breaks: 2 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'GLN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 830 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 16, 'rna3p_pyr': 18} Link IDs: {'rna2p': 5, 'rna3p': 33} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 1.28, per 1000 atoms: 0.24 Number of scatterers: 5424 At special positions: 0 Unit cell: (67.97, 82.535, 105.839, 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 P 39 15.00 O 1103 8.00 N 939 7.00 C 3314 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: 0.43 Conformation dependent library (CDL) restraints added in 173.4 milliseconds 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 6 sheets defined 41.8% alpha, 14.0% beta 11 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 86 through 98 removed outlier: 3.752A pdb=" N TYR A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 121 through 124 removed outlier: 3.764A pdb=" N GLU A 124 " --> pdb=" O TYR A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 124' Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.564A pdb=" N PHE A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.673A pdb=" N LEU A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 199 removed outlier: 3.509A pdb=" N HIS A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 4.032A pdb=" N TYR A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.985A pdb=" N ILE A 246 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.588A pdb=" N MET A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.651A pdb=" N LYS A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 309 removed outlier: 5.505A pdb=" N GLY A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 removed outlier: 3.590A pdb=" N GLU A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.937A pdb=" N HIS A 385 " --> pdb=" O HIS A 382 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 387 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 4.078A pdb=" N PHE A 393 " --> pdb=" O PRO A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 405 removed outlier: 3.632A pdb=" N HIS A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 529 through 538 removed outlier: 4.088A pdb=" N ILE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.554A pdb=" N LEU A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 623 through 632 removed outlier: 3.578A pdb=" N LYS A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 629 " --> pdb=" O GLU A 625 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.809A pdb=" N LYS A 640 " --> pdb=" O PHE A 637 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 641 " --> pdb=" O PHE A 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 637 through 641' Processing helix chain 'A' and resid 642 through 650 Processing helix chain 'A' and resid 691 through 702 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.740A pdb=" N THR A 77 " --> pdb=" O GLN A 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.676A pdb=" N PHE A 422 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.966A pdb=" N LYS A 429 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLY A 314 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP A 263 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 315 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 181 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE A 236 " --> pdb=" O THR A 583 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N THR A 583 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL A 238 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AA5, first strand: chain 'A' and resid 521 through 522 removed outlier: 6.739A pdb=" N LEU A 560 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS A 589 " --> pdb=" O ARG A 602 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG A 602 " --> pdb=" O CYS A 589 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 655 through 658 removed outlier: 3.887A pdb=" N GLY A 655 " --> pdb=" O ARG A 681 " (cutoff:3.500A) 159 hydrogen bonds defined for protein. 435 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1575 1.34 - 1.46: 1238 1.46 - 1.58: 2698 1.58 - 1.70: 76 1.70 - 1.82: 49 Bond restraints: 5636 Sorted by residual: bond pdb=" C PRO A 663 " pdb=" O PRO A 663 " ideal model delta sigma weight residual 1.235 1.216 0.019 1.30e-02 5.92e+03 2.15e+00 bond pdb=" C GLU A 662 " pdb=" N PRO A 663 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.42e+00 bond pdb=" N1 U B 84 " pdb=" C2 U B 84 " ideal model delta sigma weight residual 1.381 1.391 -0.010 9.00e-03 1.23e+04 1.36e+00 bond pdb=" CB ASP A 378 " pdb=" CG ASP A 378 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" CA PRO A 663 " pdb=" C PRO A 663 " ideal model delta sigma weight residual 1.520 1.533 -0.014 1.42e-02 4.96e+03 9.46e-01 ... (remaining 5631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 7542 1.68 - 3.36: 264 3.36 - 5.04: 26 5.04 - 6.72: 8 6.72 - 8.39: 1 Bond angle restraints: 7841 Sorted by residual: angle pdb=" C1' C B 82 " pdb=" N1 C B 82 " pdb=" C2 C B 82 " ideal model delta sigma weight residual 118.80 123.94 -5.14 1.10e+00 8.26e-01 2.18e+01 angle pdb=" O5' G B 81 " pdb=" C5' G B 81 " pdb=" C4' G B 81 " ideal model delta sigma weight residual 109.40 112.10 -2.70 8.00e-01 1.56e+00 1.14e+01 angle pdb=" O5' U B 94 " pdb=" C5' U B 94 " pdb=" C4' U B 94 " ideal model delta sigma weight residual 109.40 112.10 -2.70 8.00e-01 1.56e+00 1.14e+01 angle pdb=" C1' C B 82 " pdb=" N1 C B 82 " pdb=" C6 C B 82 " ideal model delta sigma weight residual 120.80 116.79 4.01 1.20e+00 6.94e-01 1.11e+01 angle pdb=" O5' G B 87 " pdb=" C5' G B 87 " pdb=" C4' G B 87 " ideal model delta sigma weight residual 109.40 112.06 -2.66 8.00e-01 1.56e+00 1.11e+01 ... (remaining 7836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.43: 3283 30.43 - 60.86: 163 60.86 - 91.29: 41 91.29 - 121.72: 0 121.72 - 152.16: 1 Dihedral angle restraints: 3488 sinusoidal: 1794 harmonic: 1694 Sorted by residual: dihedral pdb=" O4' C B 82 " pdb=" C1' C B 82 " pdb=" N1 C B 82 " pdb=" C2 C B 82 " ideal model delta sinusoidal sigma weight residual 200.00 47.84 152.16 1 1.50e+01 4.44e-03 8.04e+01 dihedral pdb=" CA GLY A 156 " pdb=" C GLY A 156 " pdb=" N ASN A 157 " pdb=" CA ASN A 157 " ideal model delta harmonic sigma weight residual -180.00 -161.24 -18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLY A 156 " pdb=" CA GLY A 156 " ideal model delta harmonic sigma weight residual -180.00 -163.04 -16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 3485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 546 0.031 - 0.062: 212 0.062 - 0.093: 76 0.093 - 0.124: 36 0.124 - 0.155: 41 Chirality restraints: 911 Sorted by residual: chirality pdb=" CA ILE A 523 " pdb=" N ILE A 523 " pdb=" C ILE A 523 " pdb=" CB ILE A 523 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" C2' C B 82 " pdb=" C3' C B 82 " pdb=" O2' C B 82 " pdb=" C1' C B 82 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" C1' C B 82 " pdb=" O4' C B 82 " pdb=" C2' C B 82 " pdb=" N1 C B 82 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 908 not shown) Planarity restraints: 858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 531 " -0.024 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO A 532 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 532 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 532 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 540 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 541 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 541 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 541 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 662 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C GLU A 662 " -0.023 2.00e-02 2.50e+03 pdb=" O GLU A 662 " 0.008 2.00e-02 2.50e+03 pdb=" N PRO A 663 " 0.008 2.00e-02 2.50e+03 ... (remaining 855 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 2755 3.01 - 3.48: 5189 3.48 - 3.96: 8578 3.96 - 4.43: 9292 4.43 - 4.90: 14333 Nonbonded interactions: 40147 Sorted by model distance: nonbonded pdb=" O2' SAM A 801 " pdb=" O3' SAM A 801 " model vdw 2.541 2.432 nonbonded pdb=" N1 G B 1 " pdb=" C4 G B 1 " model vdw 2.580 2.672 nonbonded pdb=" O4' U B 84 " pdb=" C6 U B 84 " model vdw 2.586 2.672 nonbonded pdb=" OG1 THR A 77 " pdb=" O GLN A 161 " model vdw 2.589 3.040 nonbonded pdb=" N1 G B 7 " pdb=" C4 G B 7 " model vdw 2.592 2.672 ... (remaining 40142 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 individual isotropic 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: 1.500 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: 0.020 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.570 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 0.028 5636 Z= 0.135 Angle : 0.661 8.394 7841 Z= 0.409 Chirality : 0.049 0.155 911 Planarity : 0.005 0.035 858 Dihedral : 17.297 152.156 2386 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.03 (0.36), residues: 573 helix: 0.88 (0.41), residues: 185 sheet: -0.74 (0.49), residues: 102 loop : -0.14 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 695 TYR 0.009 0.001 TYR A 83 PHE 0.007 0.001 PHE A 66 TRP 0.008 0.001 TRP A 284 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 ( 5636) covalent geometry : angle 0.66108 / 0.41 ( 7841) hydrogen bonds : bond 0.22614 / 15.49 ( 185) hydrogen bonds : angle 6.96572 / 4.86 ( 491) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LYS cc_start: 0.9166 (mmtp) cc_final: 0.8932 (mmtm) REVERT: A 324 ASN cc_start: 0.9238 (t0) cc_final: 0.8982 (t0) REVERT: A 579 LYS cc_start: 0.9218 (ttmt) cc_final: 0.8985 (ttpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0629 time to fit residues: 6.3752 Evaluate side-chains 52 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.077290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.055816 restraints weight = 16597.570| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 4.52 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5636 Z= 0.161 Angle : 0.580 7.999 7841 Z= 0.298 Chirality : 0.041 0.173 911 Planarity : 0.005 0.043 858 Dihedral : 17.070 153.710 1267 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.42 % Allowed : 8.48 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.21 (0.37), residues: 573 helix: 1.29 (0.42), residues: 189 sheet: -0.48 (0.49), residues: 99 loop : -0.33 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 389 TYR 0.021 0.001 TYR A 698 PHE 0.023 0.001 PHE A 530 TRP 0.006 0.001 TRP A 127 HIS 0.007 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 5636) covalent geometry : angle 0.57973 / 0.30 ( 7841) hydrogen bonds : bond 0.05427 / 3.72 ( 185) hydrogen bonds : angle 5.28040 / 3.70 ( 491) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8841 (mm-30) REVERT: A 183 MET cc_start: 0.9002 (mtp) cc_final: 0.8516 (mtm) REVERT: A 221 CYS cc_start: 0.9463 (m) cc_final: 0.9126 (m) REVERT: A 257 LYS cc_start: 0.9279 (mmtp) cc_final: 0.9063 (mmtm) REVERT: A 324 ASN cc_start: 0.9641 (t0) cc_final: 0.8540 (t0) REVERT: A 392 MET cc_start: 0.9165 (mtt) cc_final: 0.8796 (mtt) REVERT: A 579 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8599 (ttpp) outliers start: 12 outliers final: 9 residues processed: 55 average time/residue: 0.0644 time to fit residues: 5.0259 Evaluate side-chains 54 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 651 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 6.9990 chunk 9 optimal weight: 0.0980 chunk 6 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 30.0000 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 291 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.074266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.052927 restraints weight = 16905.860| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 4.44 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5636 Z= 0.221 Angle : 0.609 6.763 7841 Z= 0.311 Chirality : 0.043 0.248 911 Planarity : 0.005 0.042 858 Dihedral : 16.870 151.263 1267 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.42 % Allowed : 11.52 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.05 (0.36), residues: 573 helix: 1.22 (0.43), residues: 183 sheet: -0.52 (0.50), residues: 99 loop : -0.47 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 551 TYR 0.019 0.002 TYR A 698 PHE 0.016 0.001 PHE A 530 TRP 0.007 0.001 TRP A 127 HIS 0.005 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 ( 5636) covalent geometry : angle 0.60930 / 0.31 ( 7841) hydrogen bonds : bond 0.05530 / 3.80 ( 185) hydrogen bonds : angle 5.02373 / 3.47 ( 491) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8830 (mm-30) REVERT: A 183 MET cc_start: 0.9090 (mtp) cc_final: 0.8655 (mtm) REVERT: A 221 CYS cc_start: 0.9539 (m) cc_final: 0.9213 (m) REVERT: A 392 MET cc_start: 0.9176 (mtt) cc_final: 0.8811 (mtt) outliers start: 12 outliers final: 8 residues processed: 51 average time/residue: 0.0740 time to fit residues: 5.1796 Evaluate side-chains 48 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 651 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 35 optimal weight: 0.0050 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.054813 restraints weight = 16642.133| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 4.48 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5636 Z= 0.101 Angle : 0.531 8.010 7841 Z= 0.264 Chirality : 0.039 0.126 911 Planarity : 0.005 0.039 858 Dihedral : 16.775 150.743 1267 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.62 % Allowed : 12.73 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.20 (0.37), residues: 573 helix: 1.28 (0.43), residues: 184 sheet: -0.17 (0.54), residues: 93 loop : -0.45 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 545 TYR 0.018 0.001 TYR A 698 PHE 0.022 0.001 PHE A 530 TRP 0.005 0.001 TRP A 127 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 5636) covalent geometry : angle 0.53066 / 0.26 ( 7841) hydrogen bonds : bond 0.04111 / 2.85 ( 185) hydrogen bonds : angle 4.54083 / 3.16 ( 491) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8753 (mm-30) REVERT: A 183 MET cc_start: 0.9007 (mtp) cc_final: 0.8644 (mtm) REVERT: A 221 CYS cc_start: 0.9517 (m) cc_final: 0.9181 (m) REVERT: A 324 ASN cc_start: 0.9470 (t0) cc_final: 0.9057 (t0) REVERT: A 392 MET cc_start: 0.9163 (mtt) cc_final: 0.8779 (mtt) REVERT: A 549 LEU cc_start: 0.9797 (pt) cc_final: 0.8882 (tt) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.0633 time to fit residues: 4.3827 Evaluate side-chains 46 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 692 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 0.2980 chunk 57 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.075903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.054303 restraints weight = 17127.268| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 4.54 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5636 Z= 0.110 Angle : 0.512 6.397 7841 Z= 0.257 Chirality : 0.039 0.139 911 Planarity : 0.004 0.037 858 Dihedral : 16.656 149.969 1267 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.62 % Allowed : 14.14 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.23 (0.37), residues: 573 helix: 1.35 (0.43), residues: 184 sheet: -0.13 (0.54), residues: 93 loop : -0.47 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 695 TYR 0.014 0.001 TYR A 698 PHE 0.014 0.001 PHE A 530 TRP 0.005 0.001 TRP A 284 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 5636) covalent geometry : angle 0.51203 / 0.26 ( 7841) hydrogen bonds : bond 0.04008 / 2.75 ( 185) hydrogen bonds : angle 4.39683 / 3.05 ( 491) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8758 (mm-30) REVERT: A 183 MET cc_start: 0.8987 (mtp) cc_final: 0.8595 (mtm) REVERT: A 221 CYS cc_start: 0.9518 (m) cc_final: 0.9186 (m) REVERT: A 324 ASN cc_start: 0.9435 (t0) cc_final: 0.8790 (t0) REVERT: A 327 GLU cc_start: 0.8129 (pm20) cc_final: 0.7908 (pm20) REVERT: A 392 MET cc_start: 0.9175 (mtt) cc_final: 0.8787 (mtt) outliers start: 8 outliers final: 7 residues processed: 47 average time/residue: 0.0703 time to fit residues: 4.5920 Evaluate side-chains 48 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 692 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 19 optimal weight: 0.0070 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.076398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.054855 restraints weight = 16878.813| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 4.54 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5636 Z= 0.099 Angle : 0.507 7.911 7841 Z= 0.253 Chirality : 0.038 0.126 911 Planarity : 0.004 0.036 858 Dihedral : 16.625 149.945 1267 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.02 % Allowed : 14.75 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.27 (0.37), residues: 573 helix: 1.39 (0.43), residues: 184 sheet: -0.06 (0.55), residues: 93 loop : -0.46 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 568 TYR 0.013 0.001 TYR A 698 PHE 0.011 0.001 PHE A 530 TRP 0.011 0.001 TRP A 373 HIS 0.003 0.000 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 5636) covalent geometry : angle 0.50734 / 0.25 ( 7841) hydrogen bonds : bond 0.03728 / 2.55 ( 185) hydrogen bonds : angle 4.25724 / 2.96 ( 491) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.9309 (mm-30) cc_final: 0.8803 (mm-30) REVERT: A 183 MET cc_start: 0.8966 (mtp) cc_final: 0.8603 (mtm) REVERT: A 221 CYS cc_start: 0.9512 (m) cc_final: 0.9185 (m) REVERT: A 324 ASN cc_start: 0.9440 (t0) cc_final: 0.8805 (t0) REVERT: A 392 MET cc_start: 0.9166 (mtt) cc_final: 0.8736 (mtt) outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 0.0679 time to fit residues: 4.6927 Evaluate side-chains 49 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 651 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.076575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.054910 restraints weight = 16897.820| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 4.50 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5636 Z= 0.097 Angle : 0.512 7.723 7841 Z= 0.254 Chirality : 0.038 0.126 911 Planarity : 0.004 0.036 858 Dihedral : 16.586 149.516 1267 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.62 % Allowed : 15.96 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.34 (0.37), residues: 573 helix: 1.43 (0.43), residues: 184 sheet: -0.06 (0.55), residues: 94 loop : -0.41 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 568 TYR 0.012 0.001 TYR A 698 PHE 0.011 0.001 PHE A 530 TRP 0.007 0.001 TRP A 284 HIS 0.002 0.000 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 5636) covalent geometry : angle 0.51167 / 0.25 ( 7841) hydrogen bonds : bond 0.03601 / 2.44 ( 185) hydrogen bonds : angle 4.15477 / 2.89 ( 491) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8719 (mm-30) REVERT: A 183 MET cc_start: 0.8948 (mtp) cc_final: 0.8568 (mtm) REVERT: A 221 CYS cc_start: 0.9514 (m) cc_final: 0.9186 (m) REVERT: A 257 LYS cc_start: 0.9464 (mmtm) cc_final: 0.9161 (mmmt) REVERT: A 324 ASN cc_start: 0.9488 (t0) cc_final: 0.9130 (t0) REVERT: A 392 MET cc_start: 0.9165 (mtt) cc_final: 0.8726 (mtt) outliers start: 8 outliers final: 7 residues processed: 45 average time/residue: 0.0704 time to fit residues: 4.4532 Evaluate side-chains 45 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 565 LYS Chi-restraints excluded: chain A residue 651 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 0.1980 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 23 optimal weight: 0.0030 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.077066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.055274 restraints weight = 16528.980| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 4.51 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5636 Z= 0.090 Angle : 0.532 11.012 7841 Z= 0.260 Chirality : 0.038 0.199 911 Planarity : 0.004 0.036 858 Dihedral : 16.564 149.475 1267 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.82 % Allowed : 17.17 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.43 (0.37), residues: 573 helix: 1.57 (0.43), residues: 183 sheet: 0.03 (0.56), residues: 94 loop : -0.41 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 568 TYR 0.011 0.001 TYR A 698 PHE 0.010 0.001 PHE A 530 TRP 0.008 0.001 TRP A 373 HIS 0.002 0.000 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 ( 5636) covalent geometry : angle 0.53176 / 0.26 ( 7841) hydrogen bonds : bond 0.03339 / 2.25 ( 185) hydrogen bonds : angle 4.03922 / 2.82 ( 491) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8709 (mm-30) REVERT: A 183 MET cc_start: 0.8900 (mtp) cc_final: 0.8541 (mtm) REVERT: A 221 CYS cc_start: 0.9500 (m) cc_final: 0.9166 (m) REVERT: A 257 LYS cc_start: 0.9444 (mmtm) cc_final: 0.9167 (mmmt) REVERT: A 324 ASN cc_start: 0.9491 (t0) cc_final: 0.9107 (t0) REVERT: A 392 MET cc_start: 0.9157 (mtt) cc_final: 0.8702 (mtt) outliers start: 9 outliers final: 8 residues processed: 48 average time/residue: 0.0551 time to fit residues: 3.9147 Evaluate side-chains 50 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 651 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 41 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 0.0570 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 0.0070 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.056345 restraints weight = 16683.637| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 4.48 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5636 Z= 0.088 Angle : 0.523 8.358 7841 Z= 0.254 Chirality : 0.038 0.173 911 Planarity : 0.004 0.037 858 Dihedral : 16.534 149.383 1267 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.41 % Allowed : 17.78 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.47 (0.37), residues: 573 helix: 1.59 (0.44), residues: 184 sheet: 0.07 (0.56), residues: 94 loop : -0.37 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 256 TYR 0.010 0.001 TYR A 698 PHE 0.009 0.001 PHE A 530 TRP 0.007 0.001 TRP A 284 HIS 0.002 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 ( 5636) covalent geometry : angle 0.52317 / 0.25 ( 7841) hydrogen bonds : bond 0.03139 / 2.10 ( 185) hydrogen bonds : angle 3.95208 / 2.77 ( 491) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.9337 (mm-30) cc_final: 0.8749 (mm-30) REVERT: A 183 MET cc_start: 0.8902 (mtp) cc_final: 0.8522 (mtm) REVERT: A 221 CYS cc_start: 0.9508 (m) cc_final: 0.9234 (m) REVERT: A 257 LYS cc_start: 0.9452 (mmtm) cc_final: 0.9162 (mmmt) REVERT: A 324 ASN cc_start: 0.9503 (t0) cc_final: 0.9132 (t0) REVERT: A 392 MET cc_start: 0.9147 (mtt) cc_final: 0.8657 (mtt) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.0625 time to fit residues: 4.3065 Evaluate side-chains 49 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 433 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 7.9990 chunk 57 optimal weight: 30.0000 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.0070 chunk 11 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.076396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.055034 restraints weight = 16880.810| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 4.43 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5636 Z= 0.116 Angle : 0.534 8.510 7841 Z= 0.262 Chirality : 0.038 0.179 911 Planarity : 0.004 0.036 858 Dihedral : 16.513 148.904 1267 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.41 % Allowed : 17.98 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.49 (0.37), residues: 573 helix: 1.62 (0.44), residues: 184 sheet: 0.02 (0.56), residues: 94 loop : -0.36 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 220 TYR 0.009 0.001 TYR A 698 PHE 0.008 0.001 PHE A 530 TRP 0.009 0.001 TRP A 284 HIS 0.003 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 5636) covalent geometry : angle 0.53425 / 0.26 ( 7841) hydrogen bonds : bond 0.03582 / 2.39 ( 185) hydrogen bonds : angle 4.00619 / 2.80 ( 491) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.8890 (mtp) cc_final: 0.8504 (mtm) REVERT: A 221 CYS cc_start: 0.9523 (m) cc_final: 0.9210 (m) REVERT: A 257 LYS cc_start: 0.9448 (mmtm) cc_final: 0.9183 (mmmt) REVERT: A 324 ASN cc_start: 0.9512 (t0) cc_final: 0.9132 (t0) REVERT: A 392 MET cc_start: 0.9148 (mtt) cc_final: 0.8663 (mtt) outliers start: 7 outliers final: 7 residues processed: 43 average time/residue: 0.0656 time to fit residues: 4.1903 Evaluate side-chains 47 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 433 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.077634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.056150 restraints weight = 16764.695| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 4.49 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5636 Z= 0.091 Angle : 0.525 8.049 7841 Z= 0.255 Chirality : 0.038 0.176 911 Planarity : 0.004 0.037 858 Dihedral : 16.534 149.195 1267 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.41 % Allowed : 18.18 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 are not related in a simple way. whole: 0.53 (0.37), residues: 573 helix: 1.60 (0.43), residues: 184 sheet: 0.12 (0.56), residues: 94 loop : -0.31 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 278 TYR 0.010 0.001 TYR A 698 PHE 0.008 0.001 PHE A 530 TRP 0.007 0.001 TRP A 373 HIS 0.002 0.000 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 ( 5636) covalent geometry : angle 0.52475 / 0.25 ( 7841) hydrogen bonds : bond 0.03290 / 2.19 ( 185) hydrogen bonds : angle 3.91684 / 2.75 ( 491) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1187.60 seconds wall clock time: 21 minutes 8.58 seconds (1268.58 seconds total)