Starting phenix.real_space_refine on Thu Jul 2 11:50:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lzu_63531/07_2026/9lzu_63531.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lzu_63531/07_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_63531/07_2026/9lzu_63531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lzu_63531/07_2026/9lzu_63531.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lzu_63531/07_2026/9lzu_63531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lzu_63531/07_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-dev-6108/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: 1.59, per 1000 atoms: 0.19 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: 0.82 Conformation dependent library (CDL) restraints added in 200.9 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: 0.98 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: 1.52 Time building geometry restraints manager: 1.09 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 1.50e-02 4.44e+03 1.57e+01 bond pdb=" O3' G C 19 " pdb=" P G C 20 " ideal model delta sigma weight residual 1.607 1.561 0.046 1.50e-02 4.44e+03 9.35e+00 bond pdb=" O3' U C 17 " pdb=" P C C 18 " ideal model delta sigma weight residual 1.607 1.564 0.043 1.50e-02 4.44e+03 8.35e+00 bond pdb=" O3' G C 22 " pdb=" P U C 23 " ideal model delta sigma weight residual 1.607 1.568 0.039 1.50e-02 4.44e+03 6.74e+00 bond pdb=" O3' A C 28 " pdb=" P A C 29 " ideal model delta sigma weight residual 1.607 1.573 0.034 1.50e-02 4.44e+03 5.25e+00 ... (remaining 8647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 11681 1.14 - 2.29: 209 2.29 - 3.43: 50 3.43 - 4.57: 18 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=" 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 1.50e+00 4.44e-01 1.33e+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 ... (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: 1146 0.049 - 0.098: 173 0.098 - 0.146: 34 0.146 - 0.195: 5 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.080 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.500 ------------------------------------------------------------------------------- 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= 0.162 Angle : 0.447 5.717 11968 Z= 0.305 Chirality : 0.039 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 0.00252 / 0.16 ( 8652) covalent geometry : angle 0.44716 / 0.30 (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 : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8259 (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: 0.7506 (pp) REVERT: A 648 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.6645 (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: 0.1447 time to fit residues: 33.4956 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 : 0.290 ------------------------------------------------------------------------------- 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 432 ASN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.067002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.057920 restraints weight = 23430.449| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.93 r_work: 0.2742 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8652 Z= 0.242 Angle : 0.662 7.413 11968 Z= 0.363 Chirality : 0.042 0.201 1360 Planarity : 0.005 0.062 1301 Dihedral : 17.426 178.233 1952 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.14 % Favored : 93.74 % Rotamer: Outliers : 3.20 % Allowed : 11.08 % Favored : 85.71 % 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: 0.31 (0.29), residues: 847 helix: 1.27 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.72 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 333 TYR 0.022 0.003 TYR A 708 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 0.00541 / 0.24 ( 8652) covalent geometry : angle 0.66208 / 0.36 (11968) hydrogen bonds : bond 0.05551 / 3.73 ( 430) hydrogen bonds : angle 4.18947 / 2.93 ( 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 141 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8354 (t0) cc_final: 0.7955 (t0) REVERT: A 408 ASP cc_start: 0.8120 (m-30) cc_final: 0.7882 (m-30) REVERT: A 416 TYR cc_start: 0.7107 (t80) cc_final: 0.6819 (t80) REVERT: A 900 TYR cc_start: 0.8254 (t80) cc_final: 0.7853 (t80) outliers start: 24 outliers final: 10 residues processed: 135 average time/residue: 0.1073 time to fit residues: 19.0464 Evaluate side-chains 108 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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: 0.9980 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS ** A 432 ASN ** 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 = 0.3061 r_free = 0.3061 target = 0.066726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.057666 restraints weight = 23474.796| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.93 r_work: 0.2737 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8652 Z= 0.139 Angle : 0.513 7.104 11968 Z= 0.287 Chirality : 0.036 0.187 1360 Planarity : 0.004 0.046 1301 Dihedral : 17.371 179.716 1951 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.79 % Favored : 94.10 % Rotamer: Outliers : 2.94 % Allowed : 13.08 % Favored : 83.98 % 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: 0.58 (0.29), residues: 847 helix: 1.47 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.59 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 454 TYR 0.016 0.002 TYR A 708 PHE 0.011 0.001 PHE A 591 TRP 0.020 0.002 TRP A 423 HIS 0.005 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 8652) covalent geometry : angle 0.51310 / 0.29 (11968) hydrogen bonds : bond 0.04626 / 3.07 ( 430) hydrogen bonds : angle 4.09825 / 2.84 ( 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 120 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8882 (ttpp) REVERT: A 377 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8364 (ttpp) REVERT: A 407 ASN cc_start: 0.8325 (t0) cc_final: 0.8033 (t0) REVERT: A 410 GLN cc_start: 0.7922 (mt0) cc_final: 0.7621 (mt0) REVERT: A 900 TYR cc_start: 0.8480 (t80) cc_final: 0.8112 (t80) REVERT: A 952 GLU cc_start: 0.8775 (mp0) cc_final: 0.8425 (mp0) outliers start: 22 outliers final: 14 residues processed: 115 average time/residue: 0.1059 time to fit residues: 16.1764 Evaluate side-chains 109 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU 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 362 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 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: 2.9990 chunk 0 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 ASN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 951 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.059737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.050996 restraints weight = 24001.901| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 1.92 r_work: 0.2571 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8652 Z= 0.264 Angle : 0.656 8.476 11968 Z= 0.366 Chirality : 0.043 0.193 1360 Planarity : 0.005 0.043 1301 Dihedral : 17.607 179.987 1951 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.32 % Favored : 92.56 % Rotamer: Outliers : 4.54 % Allowed : 12.68 % Favored : 82.78 % 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: 0.11 (0.28), residues: 847 helix: 1.11 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.79 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 899 TYR 0.023 0.003 TYR A 708 PHE 0.020 0.002 PHE A 857 TRP 0.011 0.003 TRP A 423 HIS 0.013 0.002 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.26 ( 8652) covalent geometry : angle 0.65637 / 0.37 (11968) hydrogen bonds : bond 0.05872 / 3.98 ( 430) hydrogen bonds : angle 4.43856 / 3.11 ( 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 125 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8870 (ttpp) REVERT: A 334 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6526 (tt0) REVERT: A 407 ASN cc_start: 0.8348 (t0) cc_final: 0.8011 (t0) REVERT: A 574 LEU cc_start: 0.8282 (mt) cc_final: 0.7878 (pp) REVERT: A 676 MET cc_start: 0.8584 (tpt) cc_final: 0.8262 (tpt) REVERT: A 782 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7669 (ptt) REVERT: A 806 LYS cc_start: 0.8857 (tptp) cc_final: 0.8604 (tptp) REVERT: A 952 GLU cc_start: 0.8938 (mp0) cc_final: 0.8555 (mp0) outliers start: 34 outliers final: 16 residues processed: 116 average time/residue: 0.1099 time to fit residues: 16.7858 Evaluate side-chains 104 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 340 LYS 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 782 MET 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: 0.0070 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.0570 chunk 66 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS ** A 432 ASN ** 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 = 0.2970 r_free = 0.2970 target = 0.062544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.053751 restraints weight = 23750.052| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.91 r_work: 0.2646 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8652 Z= 0.124 Angle : 0.522 6.816 11968 Z= 0.290 Chirality : 0.036 0.176 1360 Planarity : 0.003 0.045 1301 Dihedral : 17.521 178.914 1951 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.02 % Favored : 93.86 % Rotamer: Outliers : 2.94 % Allowed : 14.82 % Favored : 82.24 % 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: 1.39 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.56 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.014 0.001 TYR A 297 PHE 0.009 0.001 PHE A 591 TRP 0.008 0.002 TRP A 423 HIS 0.005 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 8652) covalent geometry : angle 0.52183 / 0.29 (11968) hydrogen bonds : bond 0.04554 / 3.02 ( 430) hydrogen bonds : angle 4.22758 / 2.92 ( 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 110 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8348 (t0) cc_final: 0.8031 (t0) REVERT: A 676 MET cc_start: 0.8415 (tpt) cc_final: 0.8091 (tpt) REVERT: A 952 GLU cc_start: 0.8903 (mp0) cc_final: 0.8532 (mp0) outliers start: 22 outliers final: 13 residues processed: 103 average time/residue: 0.1223 time to fit residues: 16.5138 Evaluate side-chains 97 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 150 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 0.0270 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN A 431 HIS ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.062289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.053556 restraints weight = 23707.636| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 1.91 r_work: 0.2641 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8652 Z= 0.138 Angle : 0.519 7.077 11968 Z= 0.289 Chirality : 0.036 0.175 1360 Planarity : 0.004 0.041 1301 Dihedral : 17.499 178.881 1951 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.73 % Favored : 93.15 % Rotamer: Outliers : 2.94 % Allowed : 14.55 % Favored : 82.51 % 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: 1.42 (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 0.004 0.000 ARG A 333 TYR 0.016 0.001 TYR A 297 PHE 0.010 0.001 PHE A 534 TRP 0.012 0.002 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 8652) covalent geometry : angle 0.51888 / 0.29 (11968) hydrogen bonds : bond 0.04502 / 3.00 ( 430) hydrogen bonds : angle 4.19700 / 2.90 ( 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 110 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.9103 (ttpp) cc_final: 0.8608 (ttpp) REVERT: A 334 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6477 (tt0) REVERT: A 407 ASN cc_start: 0.8382 (t0) cc_final: 0.8094 (t0) REVERT: A 474 MET cc_start: 0.8806 (mtt) cc_final: 0.8537 (mtt) REVERT: A 676 MET cc_start: 0.8436 (tpt) cc_final: 0.8088 (tpt) REVERT: A 952 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8562 (mp0) outliers start: 22 outliers final: 14 residues processed: 104 average time/residue: 0.1212 time to fit residues: 16.4914 Evaluate side-chains 99 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 334 GLU 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 Chi-restraints excluded: chain A residue 952 GLU 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: 0.7980 chunk 83 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 432 ASN ** 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 = 0.2963 r_free = 0.2963 target = 0.062189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.053444 restraints weight = 23984.310| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 1.93 r_work: 0.2639 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.4026 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= 0.136 Angle : 0.521 6.945 11968 Z= 0.289 Chirality : 0.036 0.175 1360 Planarity : 0.003 0.042 1301 Dihedral : 17.497 178.939 1951 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.38 % Favored : 93.51 % Rotamer: Outliers : 2.67 % Allowed : 15.62 % Favored : 81.71 % 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: 0.58 (0.29), residues: 847 helix: 1.44 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.52 (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 0.015 0.001 PHE A 406 TRP 0.008 0.002 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 8652) covalent geometry : angle 0.52147 / 0.29 (11968) hydrogen bonds : bond 0.04406 / 2.95 ( 430) hydrogen bonds : angle 4.19390 / 2.89 ( 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 110 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6482 (tt0) REVERT: A 407 ASN cc_start: 0.8533 (t0) cc_final: 0.8040 (t0) REVERT: A 416 TYR cc_start: 0.8035 (t80) cc_final: 0.7831 (t80) REVERT: A 676 MET cc_start: 0.8429 (tpt) cc_final: 0.8076 (tpt) REVERT: A 952 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8547 (mp0) outliers start: 20 outliers final: 12 residues processed: 102 average time/residue: 0.1105 time to fit residues: 14.7533 Evaluate side-chains 99 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TYR 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 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 Chi-restraints excluded: chain A residue 952 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 432 ASN ** 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 = 0.2923 r_free = 0.2923 target = 0.060430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.051827 restraints weight = 23971.173| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 1.87 r_work: 0.2599 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8652 Z= 0.188 Angle : 0.576 6.936 11968 Z= 0.320 Chirality : 0.038 0.172 1360 Planarity : 0.004 0.038 1301 Dihedral : 17.527 178.914 1951 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.20 % Favored : 92.68 % Rotamer: Outliers : 2.67 % Allowed : 16.02 % 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: 0.48 (0.29), residues: 847 helix: 1.40 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.57 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 218 TYR 0.016 0.002 TYR A 297 PHE 0.012 0.001 PHE A 534 TRP 0.006 0.002 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 8652) covalent geometry : angle 0.57600 / 0.32 (11968) hydrogen bonds : bond 0.04803 / 3.25 ( 430) hydrogen bonds : angle 4.28216 / 2.98 ( 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 106 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6557 (tt0) REVERT: A 407 ASN cc_start: 0.8553 (t0) cc_final: 0.7885 (t0) REVERT: A 676 MET cc_start: 0.8545 (tpt) cc_final: 0.8204 (tpt) REVERT: A 952 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8521 (mp0) outliers start: 20 outliers final: 14 residues processed: 101 average time/residue: 0.0995 time to fit residues: 13.2044 Evaluate side-chains 104 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 334 GLU 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 787 LYS Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 952 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 63 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 432 ASN ** 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 = 0.2934 r_free = 0.2934 target = 0.060890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.052210 restraints weight = 24018.813| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 1.91 r_work: 0.2609 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8652 Z= 0.154 Angle : 0.579 11.233 11968 Z= 0.320 Chirality : 0.037 0.172 1360 Planarity : 0.004 0.048 1301 Dihedral : 17.554 178.817 1951 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.97 % Favored : 92.92 % Rotamer: Outliers : 2.27 % Allowed : 16.42 % 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: 0.51 (0.29), residues: 847 helix: 1.42 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.56 (0.34), 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 0.006 0.001 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 8652) covalent geometry : angle 0.57907 / 0.32 (11968) hydrogen bonds : bond 0.04598 / 3.11 ( 430) hydrogen bonds : angle 4.28478 / 2.97 ( 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 104 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6353 (tt0) REVERT: A 410 GLN cc_start: 0.8622 (mp10) cc_final: 0.8417 (pm20) REVERT: A 676 MET cc_start: 0.8519 (tpt) cc_final: 0.8195 (tpt) REVERT: A 776 LYS cc_start: 0.8474 (mtmm) cc_final: 0.8087 (mtpt) REVERT: A 952 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8547 (mp0) outliers start: 17 outliers final: 13 residues processed: 101 average time/residue: 0.1091 time to fit residues: 14.5036 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 : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TYR 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 351 VAL 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 Chi-restraints excluded: chain A residue 952 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.0010 chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 432 ASN ** 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 = 0.2941 r_free = 0.2941 target = 0.061179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.052526 restraints weight = 23755.284| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 1.90 r_work: 0.2618 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.4269 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= 0.145 Angle : 0.573 9.107 11968 Z= 0.316 Chirality : 0.037 0.173 1360 Planarity : 0.004 0.049 1301 Dihedral : 17.542 178.618 1951 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.20 % Favored : 92.68 % Rotamer: Outliers : 2.00 % Allowed : 16.69 % 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: 1.46 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.52 (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 0.006 0.001 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8652) covalent geometry : angle 0.57321 / 0.32 (11968) hydrogen bonds : bond 0.04449 / 3.00 ( 430) hydrogen bonds : angle 4.26637 / 2.95 ( 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 103 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6318 (tt0) REVERT: A 676 MET cc_start: 0.8480 (tpt) cc_final: 0.8159 (tpt) REVERT: A 776 LYS cc_start: 0.8478 (mtmm) cc_final: 0.8129 (mtmt) REVERT: A 952 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8528 (mp0) outliers start: 15 outliers final: 12 residues processed: 99 average time/residue: 0.0947 time to fit residues: 12.4233 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 : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TYR 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 351 VAL 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 Chi-restraints excluded: chain A residue 952 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 33 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 67 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** 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 = 0.2938 r_free = 0.2938 target = 0.061030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.052420 restraints weight = 23945.015| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 1.90 r_work: 0.2615 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8652 Z= 0.147 Angle : 0.568 8.752 11968 Z= 0.314 Chirality : 0.037 0.173 1360 Planarity : 0.004 0.048 1301 Dihedral : 17.534 178.695 1951 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.08 % Favored : 92.80 % Rotamer: Outliers : 2.00 % Allowed : 16.82 % Favored : 81.17 % 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: 0.60 (0.29), residues: 847 helix: 1.47 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.48 (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 0.011 0.001 PHE A 406 TRP 0.005 0.001 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 8652) covalent geometry : angle 0.56838 / 0.31 (11968) hydrogen bonds : bond 0.04437 / 2.99 ( 430) hydrogen bonds : angle 4.26766 / 2.96 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1733.54 seconds wall clock time: 30 minutes 27.36 seconds (1827.36 seconds total)