Starting phenix.real_space_refine on Wed Aug 5 04:32:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lzu_63531/08_2026/9lzu_63531.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lzu_63531/08_2026/9lzu_63531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lzu_63531/08_2026/9lzu_63531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lzu_63531/08_2026/9lzu_63531.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lzu_63531/08_2026/9lzu_63531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lzu_63531/08_2026/9lzu_63531.map" } resolution = 3.1 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= 0.004 sd= 0.479 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: 6 Type Number sf(0) Gaussians P 65 5.49 5 Mg 1 5.21 5 S 25 5.16 5 C 5067 2.51 5 N 1442 2.21 5 O 1764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 8364 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 6978 Classifications: {'peptide': 853} Link IDs: {'PTRANS': 14, 'TRANS': 838} Chain breaks: 2 Chain: "C" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1083 Classifications: {'RNA': 51} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p_pur': 21, 'rna3p_pyr': 22} Link IDs: {'rna2p': 8, 'rna3p': 42} Chain: "B" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 302 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 6} Link IDs: {'rna3p': 13} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.78, per 1000 atoms: 0.21 Number of scatterers: 8364 At special positions: 0 Unit cell: (95.76, 95.76, 121.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 65 15.00 Mg 1 11.99 O 1764 8.00 N 1442 7.00 C 5067 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: 0.64 Conformation dependent library (CDL) restraints added in 208.8 milliseconds 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1634 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 1 sheets defined 70.8% alpha, 0.7% beta 19 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 118 through 149 Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.574A pdb=" N ASN A 180 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 202 Processing helix chain 'A' and resid 203 through 207 removed outlier: 3.608A pdb=" N GLY A 206 " --> pdb=" O PRO A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 224 through 244 Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 265 through 289 removed outlier: 3.818A pdb=" N ILE A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.109A pdb=" N TYR A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 332 through 337 removed outlier: 3.517A pdb=" N LEU A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 355 through 379 removed outlier: 3.642A pdb=" N VAL A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N THR A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 405 removed outlier: 3.678A pdb=" N ILE A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 416 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 425 through 433 Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 506 Proline residue: A 503 - end of helix Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 520 through 536 removed outlier: 3.814A pdb=" N PHE A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 557 removed outlier: 3.579A pdb=" N TYR A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 573 removed outlier: 3.935A pdb=" N LYS A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 620 through 635 removed outlier: 4.427A pdb=" N GLN A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 654 Processing helix chain 'A' and resid 661 through 674 Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.558A pdb=" N LYS A 684 " --> pdb=" O GLN A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 690 Processing helix chain 'A' and resid 695 through 744 removed outlier: 3.525A pdb=" N TYR A 726 " --> pdb=" O ILE A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 766 removed outlier: 3.663A pdb=" N GLY A 766 " --> pdb=" O LYS A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 789 removed outlier: 4.278A pdb=" N ARG A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 793 Processing helix chain 'A' and resid 796 through 801 removed outlier: 3.520A pdb=" N TYR A 801 " --> pdb=" O ASN A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 827 removed outlier: 3.728A pdb=" N THR A 827 " --> pdb=" O GLU A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 847 removed outlier: 3.636A pdb=" N LEU A 847 " --> pdb=" O ARG A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 863 Processing helix chain 'A' and resid 865 through 870 Processing helix chain 'A' and resid 882 through 900 Processing helix chain 'A' and resid 905 through 917 Processing helix chain 'A' and resid 921 through 930 Processing helix chain 'A' and resid 931 through 933 No H-bonds generated for 'chain 'A' and resid 931 through 933' Processing helix chain 'A' and resid 935 through 942 Processing helix chain 'A' and resid 950 through 955 removed outlier: 3.896A pdb=" N ALA A 954 " --> pdb=" O ASN A 951 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 213 through 216 removed outlier: 3.558A pdb=" N GLU A 216 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN A 219 " --> pdb=" O GLU A 216 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1110 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1874 1.33 - 1.45: 2169 1.45 - 1.57: 4443 1.57 - 1.69: 124 1.69 - 1.81: 42 Bond restraints: 8652 Sorted by residual: bond pdb=" O3' C C 18 " pdb=" P G C 19 " ideal model delta sigma weight residual 1.607 1.548 0.059 1.20e-02 6.94e+03 2.45e+01 bond pdb=" O3' G C 19 " pdb=" P G C 20 " ideal model delta sigma weight residual 1.607 1.561 0.046 1.20e-02 6.94e+03 1.46e+01 bond pdb=" O3' U C 17 " pdb=" P C C 18 " ideal model delta sigma weight residual 1.607 1.564 0.043 1.20e-02 6.94e+03 1.31e+01 bond pdb=" O3' G C 22 " pdb=" P U C 23 " ideal model delta sigma weight residual 1.607 1.568 0.039 1.20e-02 6.94e+03 1.05e+01 bond pdb=" O3' A C 28 " pdb=" P A C 29 " ideal model delta sigma weight residual 1.607 1.573 0.034 1.20e-02 6.94e+03 8.20e+00 ... (remaining 8647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 11539 1.14 - 2.29: 297 2.29 - 3.43: 103 3.43 - 4.57: 19 4.57 - 5.72: 10 Bond angle restraints: 11968 Sorted by residual: angle pdb=" C1' C C 42 " pdb=" N1 C C 42 " pdb=" C2 C C 42 " ideal model delta sigma weight residual 118.80 124.14 -5.34 1.10e+00 8.26e-01 2.36e+01 angle pdb=" N1 C C 42 " pdb=" C2 C C 42 " pdb=" O2 C C 42 " ideal model delta sigma weight residual 118.90 121.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N GLY A 478 " pdb=" CA GLY A 478 " pdb=" C GLY A 478 " ideal model delta sigma weight residual 112.50 116.76 -4.26 1.16e+00 7.43e-01 1.35e+01 angle pdb=" O2 C C 42 " pdb=" C2 C C 42 " pdb=" N3 C C 42 " ideal model delta sigma weight residual 121.90 119.37 2.53 7.00e-01 2.04e+00 1.30e+01 angle pdb=" O3' U C 25 " pdb=" C3' U C 25 " pdb=" C2' U C 25 " ideal model delta sigma weight residual 113.70 108.23 5.47 1.60e+00 3.91e-01 1.17e+01 ... (remaining 11963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 5149 35.83 - 71.65: 152 71.65 - 107.48: 20 107.48 - 143.30: 1 143.30 - 179.12: 1 Dihedral angle restraints: 5323 sinusoidal: 2788 harmonic: 2535 Sorted by residual: dihedral pdb=" O4' C C 42 " pdb=" C1' C C 42 " pdb=" N1 C C 42 " pdb=" C2 C C 42 " ideal model delta sinusoidal sigma weight residual 200.00 57.80 142.20 1 1.50e+01 4.44e-03 7.64e+01 dihedral pdb=" O4' C C 13 " pdb=" C1' C C 13 " pdb=" N1 C C 13 " pdb=" C2 C C 13 " ideal model delta sinusoidal sigma weight residual -128.00 51.12 -179.12 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA ASP A 417 " pdb=" C ASP A 417 " pdb=" N GLU A 418 " pdb=" CA GLU A 418 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1096 0.049 - 0.098: 183 0.098 - 0.146: 75 0.146 - 0.195: 4 0.195 - 0.244: 2 Chirality restraints: 1360 Sorted by residual: chirality pdb=" C3' U C 25 " pdb=" C4' U C 25 " pdb=" O3' U C 25 " pdb=" C2' U C 25 " both_signs ideal model delta sigma weight residual False -2.48 -2.72 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C3' G C 26 " pdb=" C4' G C 26 " pdb=" O3' G C 26 " pdb=" C2' G C 26 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C3' G C 22 " pdb=" C4' G C 22 " pdb=" O3' G C 22 " pdb=" C2' G C 22 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 1357 not shown) Planarity restraints: 1301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 358 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.51e+00 pdb=" C LYS A 358 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS A 358 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 359 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 417 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C ASP A 417 " 0.036 2.00e-02 2.50e+03 pdb=" O ASP A 417 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 418 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 396 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C ASP A 396 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP A 396 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 397 " -0.012 2.00e-02 2.50e+03 ... (remaining 1298 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 23 2.40 - 3.02: 4869 3.02 - 3.65: 13125 3.65 - 4.27: 19678 4.27 - 4.90: 31460 Nonbonded interactions: 69155 Sorted by model distance: nonbonded pdb=" OP1 U C 24 " pdb="MG MG C 101 " model vdw 1.771 2.170 nonbonded pdb=" O LEU A 530 " pdb=" OG SER A 533 " model vdw 2.215 3.040 nonbonded pdb=" O ALA A 567 " pdb=" OG1 THR A 571 " model vdw 2.238 3.040 nonbonded pdb=" OP2 G C 35 " pdb=" O2' A C 36 " model vdw 2.243 3.040 nonbonded pdb=" NH1 ARG A 725 " pdb=" O PHE A 948 " model vdw 2.285 3.120 ... (remaining 69150 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.200 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8652 Z= 0.195 Angle : 0.513 5.717 11968 Z= 0.357 Chirality : 0.045 0.244 1360 Planarity : 0.002 0.032 1301 Dihedral : 14.610 179.125 3689 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.07 % Allowed : 4.41 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.30), residues: 847 helix: 1.78 (0.23), residues: 536 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 546 TYR 0.010 0.001 TYR A 297 PHE 0.010 0.001 PHE A 884 TRP 0.004 0.001 TRP A 838 HIS 0.003 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.20 ( 8652) covalent geometry : angle 0.51251 / 0.36 (11968) hydrogen bonds : bond 0.13846 / 9.31 ( 430) hydrogen bonds : angle 4.61619 / 3.27 ( 1212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 183 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8258 (t) REVERT: A 374 GLU cc_start: 0.8150 (tp30) cc_final: 0.7874 (tp30) REVERT: A 407 ASN cc_start: 0.8315 (t0) cc_final: 0.8068 (t0) REVERT: A 510 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8505 (mtpp) REVERT: A 574 LEU cc_start: 0.7871 (mt) cc_final: 0.7505 (pp) REVERT: A 648 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.6644 (mpt180) REVERT: A 949 ASP cc_start: 0.8310 (t70) cc_final: 0.8066 (t0) outliers start: 8 outliers final: 2 residues processed: 189 average time/residue: 0.1306 time to fit residues: 30.4165 Evaluate side-chains 117 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 617 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN A 121 GLN A 263 ASN A 294 ASN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 ASN A 586 HIS A 595 ASN A 635 GLN A 680 GLN A 839 ASN A 871 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.067332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.058279 restraints weight = 23419.413| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.91 r_work: 0.2751 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8652 Z= 0.238 Angle : 0.664 8.691 11968 Z= 0.361 Chirality : 0.043 0.187 1360 Planarity : 0.005 0.068 1301 Dihedral : 17.445 178.323 1952 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.79 % Favored : 94.10 % Rotamer: Outliers : 3.07 % Allowed : 10.68 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.29), residues: 847 helix: 1.33 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.71 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 454 TYR 0.022 0.003 TYR A 801 PHE 0.019 0.002 PHE A 534 TRP 0.021 0.004 TRP A 423 HIS 0.008 0.002 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.24 ( 8652) covalent geometry : angle 0.66359 / 0.36 (11968) hydrogen bonds : bond 0.05419 / 3.65 ( 430) hydrogen bonds : angle 4.17841 / 2.92 ( 1212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8354 (t0) cc_final: 0.7954 (t0) REVERT: A 408 ASP cc_start: 0.8110 (m-30) cc_final: 0.7883 (m-30) REVERT: A 416 TYR cc_start: 0.7072 (t80) cc_final: 0.6778 (t80) REVERT: A 900 TYR cc_start: 0.8209 (t80) cc_final: 0.7791 (t80) outliers start: 23 outliers final: 10 residues processed: 134 average time/residue: 0.0920 time to fit residues: 16.4381 Evaluate side-chains 106 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 947 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 951 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.065458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.056458 restraints weight = 23555.527| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 1.92 r_work: 0.2709 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8652 Z= 0.169 Angle : 0.550 7.162 11968 Z= 0.306 Chirality : 0.038 0.155 1360 Planarity : 0.004 0.038 1301 Dihedral : 17.389 179.171 1951 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.14 % Favored : 93.74 % Rotamer: Outliers : 2.80 % Allowed : 12.95 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.29), residues: 847 helix: 1.43 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.63 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 421 TYR 0.017 0.002 TYR A 708 PHE 0.012 0.001 PHE A 857 TRP 0.022 0.003 TRP A 423 HIS 0.007 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 8652) covalent geometry : angle 0.54962 / 0.31 (11968) hydrogen bonds : bond 0.04883 / 3.26 ( 430) hydrogen bonds : angle 4.16420 / 2.90 ( 1212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8872 (ttpp) REVERT: A 377 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8325 (ttpp) REVERT: A 407 ASN cc_start: 0.8325 (t0) cc_final: 0.7978 (t0) REVERT: A 869 TYR cc_start: 0.9013 (m-80) cc_final: 0.8758 (m-80) REVERT: A 900 TYR cc_start: 0.8526 (t80) cc_final: 0.8170 (t80) REVERT: A 952 GLU cc_start: 0.8789 (mp0) cc_final: 0.8470 (mp0) outliers start: 21 outliers final: 13 residues processed: 115 average time/residue: 0.0986 time to fit residues: 15.1416 Evaluate side-chains 106 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 947 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.0050 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.065273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.056350 restraints weight = 23764.402| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.94 r_work: 0.2707 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8652 Z= 0.134 Angle : 0.505 6.863 11968 Z= 0.283 Chirality : 0.036 0.163 1360 Planarity : 0.003 0.040 1301 Dihedral : 17.377 178.925 1951 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.14 % Favored : 93.74 % Rotamer: Outliers : 2.94 % Allowed : 13.48 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.29), residues: 847 helix: 1.52 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.56 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 204 TYR 0.015 0.002 TYR A 708 PHE 0.011 0.001 PHE A 591 TRP 0.015 0.002 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8652) covalent geometry : angle 0.50494 / 0.28 (11968) hydrogen bonds : bond 0.04424 / 2.94 ( 430) hydrogen bonds : angle 4.14310 / 2.88 ( 1212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8301 (ttpp) REVERT: A 407 ASN cc_start: 0.8354 (t0) cc_final: 0.8047 (t0) REVERT: A 410 GLN cc_start: 0.7990 (mt0) cc_final: 0.7697 (mt0) REVERT: A 429 ILE cc_start: 0.8073 (mm) cc_final: 0.7871 (mm) REVERT: A 469 MET cc_start: 0.8931 (mmp) cc_final: 0.8578 (mmp) REVERT: A 900 TYR cc_start: 0.8618 (t80) cc_final: 0.8336 (t80) outliers start: 22 outliers final: 11 residues processed: 108 average time/residue: 0.0965 time to fit residues: 13.9041 Evaluate side-chains 98 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 947 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 44 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 ASN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.061748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.052895 restraints weight = 23744.812| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 1.92 r_work: 0.2620 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8652 Z= 0.201 Angle : 0.580 7.161 11968 Z= 0.323 Chirality : 0.040 0.163 1360 Planarity : 0.004 0.039 1301 Dihedral : 17.476 178.930 1951 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.97 % Favored : 92.92 % Rotamer: Outliers : 3.47 % Allowed : 14.15 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.38 (0.29), residues: 847 helix: 1.32 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.67 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 218 TYR 0.020 0.002 TYR A 708 PHE 0.016 0.002 PHE A 857 TRP 0.017 0.002 TRP A 423 HIS 0.006 0.002 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 ( 8652) covalent geometry : angle 0.57985 / 0.32 (11968) hydrogen bonds : bond 0.05137 / 3.47 ( 430) hydrogen bonds : angle 4.27091 / 2.98 ( 1212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6736 (tt0) REVERT: A 363 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8635 (mtm) REVERT: A 407 ASN cc_start: 0.8364 (t0) cc_final: 0.7933 (t0) REVERT: A 676 MET cc_start: 0.8515 (tpt) cc_final: 0.8161 (tpt) outliers start: 26 outliers final: 13 residues processed: 110 average time/residue: 0.0972 time to fit residues: 14.2287 Evaluate side-chains 101 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 947 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.062900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.054103 restraints weight = 23646.219| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 1.93 r_work: 0.2655 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8652 Z= 0.135 Angle : 0.528 6.683 11968 Z= 0.293 Chirality : 0.036 0.156 1360 Planarity : 0.003 0.041 1301 Dihedral : 17.459 178.305 1951 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.85 % Favored : 93.03 % Rotamer: Outliers : 2.54 % Allowed : 15.89 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.29), residues: 847 helix: 1.42 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.54 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 218 TYR 0.014 0.001 TYR A 297 PHE 0.010 0.001 PHE A 591 TRP 0.009 0.002 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 8652) covalent geometry : angle 0.52770 / 0.29 (11968) hydrogen bonds : bond 0.04469 / 2.98 ( 430) hydrogen bonds : angle 4.22737 / 2.94 ( 1212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6393 (tt0) REVERT: A 363 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8644 (mtm) REVERT: A 407 ASN cc_start: 0.8369 (t0) cc_final: 0.7950 (t0) REVERT: A 676 MET cc_start: 0.8419 (tpt) cc_final: 0.8065 (tpt) outliers start: 19 outliers final: 13 residues processed: 101 average time/residue: 0.1112 time to fit residues: 14.6506 Evaluate side-chains 99 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 947 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.062590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.053780 restraints weight = 23961.647| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 1.93 r_work: 0.2648 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8652 Z= 0.138 Angle : 0.525 7.027 11968 Z= 0.292 Chirality : 0.036 0.158 1360 Planarity : 0.004 0.042 1301 Dihedral : 17.432 178.284 1951 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.61 % Favored : 93.27 % Rotamer: Outliers : 2.67 % Allowed : 15.89 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.29), residues: 847 helix: 1.43 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.58 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 218 TYR 0.016 0.001 TYR A 297 PHE 0.009 0.001 PHE A 534 TRP 0.033 0.003 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 8652) covalent geometry : angle 0.52496 / 0.29 (11968) hydrogen bonds : bond 0.04431 / 2.96 ( 430) hydrogen bonds : angle 4.21668 / 2.92 ( 1212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6413 (tt0) REVERT: A 363 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8643 (mtm) REVERT: A 407 ASN cc_start: 0.8507 (t0) cc_final: 0.7950 (t0) REVERT: A 409 ASP cc_start: 0.8611 (t0) cc_final: 0.8398 (t0) REVERT: A 676 MET cc_start: 0.8425 (tpt) cc_final: 0.8062 (tpt) outliers start: 20 outliers final: 11 residues processed: 102 average time/residue: 0.1105 time to fit residues: 14.7953 Evaluate side-chains 99 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 947 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.062306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.053564 restraints weight = 23849.297| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 1.92 r_work: 0.2642 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8652 Z= 0.147 Angle : 0.539 7.133 11968 Z= 0.301 Chirality : 0.037 0.157 1360 Planarity : 0.004 0.042 1301 Dihedral : 17.437 178.155 1951 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.73 % Favored : 93.15 % Rotamer: Outliers : 1.87 % Allowed : 16.82 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.29), residues: 847 helix: 1.41 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.49 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 218 TYR 0.016 0.001 TYR A 297 PHE 0.009 0.001 PHE A 534 TRP 0.047 0.004 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 8652) covalent geometry : angle 0.53931 / 0.30 (11968) hydrogen bonds : bond 0.04445 / 2.99 ( 430) hydrogen bonds : angle 4.22460 / 2.93 ( 1212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6341 (tt0) REVERT: A 363 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8623 (mtm) REVERT: A 407 ASN cc_start: 0.8429 (t0) cc_final: 0.8154 (t0) REVERT: A 676 MET cc_start: 0.8439 (tpt) cc_final: 0.8072 (tpt) REVERT: A 869 TYR cc_start: 0.9042 (m-80) cc_final: 0.8840 (m-80) outliers start: 14 outliers final: 11 residues processed: 100 average time/residue: 0.1146 time to fit residues: 15.0304 Evaluate side-chains 101 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 947 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.060106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.051464 restraints weight = 24024.935| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 1.91 r_work: 0.2588 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8652 Z= 0.202 Angle : 0.602 7.205 11968 Z= 0.333 Chirality : 0.039 0.165 1360 Planarity : 0.004 0.038 1301 Dihedral : 17.493 178.443 1951 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.08 % Favored : 92.80 % Rotamer: Outliers : 1.87 % Allowed : 16.69 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.29), residues: 847 helix: 1.27 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.63 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 218 TYR 0.016 0.002 TYR A 708 PHE 0.014 0.002 PHE A 857 TRP 0.041 0.004 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 8652) covalent geometry : angle 0.60212 / 0.33 (11968) hydrogen bonds : bond 0.04966 / 3.37 ( 430) hydrogen bonds : angle 4.33197 / 3.02 ( 1212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6469 (tt0) REVERT: A 363 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8646 (mtm) REVERT: A 407 ASN cc_start: 0.8460 (t0) cc_final: 0.8068 (t0) REVERT: A 409 ASP cc_start: 0.8527 (t0) cc_final: 0.8298 (t0) REVERT: A 410 GLN cc_start: 0.8563 (mp10) cc_final: 0.8289 (mp10) REVERT: A 676 MET cc_start: 0.8592 (tpt) cc_final: 0.8239 (tpt) outliers start: 14 outliers final: 10 residues processed: 98 average time/residue: 0.1120 time to fit residues: 14.4703 Evaluate side-chains 98 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 947 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 70 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 0.0040 chunk 35 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.061410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.052777 restraints weight = 23672.403| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 1.90 r_work: 0.2623 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8652 Z= 0.149 Angle : 0.600 12.219 11968 Z= 0.331 Chirality : 0.037 0.156 1360 Planarity : 0.004 0.051 1301 Dihedral : 17.514 177.999 1951 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.20 % Favored : 92.68 % Rotamer: Outliers : 1.87 % Allowed : 17.49 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.29), residues: 847 helix: 1.38 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.44 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 218 TYR 0.016 0.001 TYR A 297 PHE 0.009 0.001 PHE A 591 TRP 0.034 0.003 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 8652) covalent geometry : angle 0.60031 / 0.33 (11968) hydrogen bonds : bond 0.04511 / 3.03 ( 430) hydrogen bonds : angle 4.30144 / 2.98 ( 1212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6309 (tt0) REVERT: A 341 ASP cc_start: 0.8130 (p0) cc_final: 0.7879 (p0) REVERT: A 363 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8635 (mtm) REVERT: A 407 ASN cc_start: 0.8475 (t0) cc_final: 0.8029 (t0) REVERT: A 410 GLN cc_start: 0.8596 (mp10) cc_final: 0.8348 (mp10) REVERT: A 676 MET cc_start: 0.8519 (tpt) cc_final: 0.8182 (tpt) REVERT: A 775 ARG cc_start: 0.5360 (mmp80) cc_final: 0.5107 (mmp80) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.1163 time to fit residues: 14.9858 Evaluate side-chains 98 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 947 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.061973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.053337 restraints weight = 23928.762| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 1.91 r_work: 0.2639 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8652 Z= 0.135 Angle : 0.572 9.032 11968 Z= 0.315 Chirality : 0.036 0.156 1360 Planarity : 0.004 0.049 1301 Dihedral : 17.486 177.900 1951 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.61 % Favored : 93.27 % Rotamer: Outliers : 1.74 % Allowed : 17.36 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.29), residues: 847 helix: 1.44 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.43 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 218 TYR 0.016 0.001 TYR A 297 PHE 0.009 0.001 PHE A 534 TRP 0.028 0.003 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 8652) covalent geometry : angle 0.57160 / 0.31 (11968) hydrogen bonds : bond 0.04318 / 2.90 ( 430) hydrogen bonds : angle 4.26838 / 2.95 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1744.16 seconds wall clock time: 30 minutes 36.40 seconds (1836.40 seconds total)