Starting phenix.real_space_refine on Wed Feb 4 02:35:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lzu_63531/02_2026/9lzu_63531.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lzu_63531/02_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_63531/02_2026/9lzu_63531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lzu_63531/02_2026/9lzu_63531.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lzu_63531/02_2026/9lzu_63531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lzu_63531/02_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 1.61, 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: 0.50 Conformation dependent library (CDL) restraints added in 157.0 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: 0.79 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: 1.20 Time building geometry restraints manager: 0.72 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=" 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=" C4' C C 18 " pdb=" C3' C C 18 " pdb=" O3' C C 18 " ideal model delta sigma weight residual 113.00 107.80 5.20 1.50e+00 4.44e-01 1.20e+01 angle pdb=" C4' G C 20 " pdb=" C3' G C 20 " pdb=" C2' G C 20 " ideal model delta sigma weight residual 102.60 99.26 3.34 1.00e+00 1.00e+00 1.12e+01 angle pdb=" C4' G C 22 " pdb=" C3' G C 22 " pdb=" O3' G C 22 " ideal model delta sigma weight residual 113.00 108.19 4.81 1.50e+00 4.44e-01 1.03e+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: 1.020 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.710 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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= 0.153 Angle : 0.447 5.717 11968 Z= 0.267 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 covalent geometry : bond 0.00251 ( 8652) covalent geometry : angle 0.44707 (11968) hydrogen bonds : bond 0.13846 ( 430) hydrogen bonds : angle 4.61619 ( 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 : 0.224 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: 0.1243 time to fit residues: 28.8347 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 : 0.293 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 121 GLN A 263 ASN A 294 ASN ** A 322 GLN ** 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 A 951 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.062824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.053872 restraints weight = 23667.915| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 1.92 r_work: 0.2643 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8652 Z= 0.246 Angle : 0.672 8.013 11968 Z= 0.359 Chirality : 0.042 0.148 1360 Planarity : 0.005 0.053 1301 Dihedral : 17.447 178.505 1952 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.73 % Favored : 93.15 % Rotamer: Outliers : 3.34 % Allowed : 10.28 % Favored : 86.38 % 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: 0.33 (0.29), residues: 847 helix: 1.15 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.49 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 204 TYR 0.028 0.003 TYR A 708 PHE 0.020 0.002 PHE A 857 TRP 0.012 0.003 TRP A 423 HIS 0.006 0.002 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 8652) covalent geometry : angle 0.67225 (11968) hydrogen bonds : bond 0.05562 ( 430) hydrogen bonds : angle 4.38791 ( 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 133 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 ASN cc_start: 0.8344 (t0) cc_final: 0.8045 (t0) REVERT: A 469 MET cc_start: 0.8956 (mmp) cc_final: 0.8636 (mmp) REVERT: A 785 ARG cc_start: 0.8281 (tmm-80) cc_final: 0.8080 (tmm-80) REVERT: A 803 ASN cc_start: 0.6775 (t0) cc_final: 0.6503 (t0) REVERT: A 900 TYR cc_start: 0.8486 (t80) cc_final: 0.7984 (t80) REVERT: A 952 GLU cc_start: 0.8827 (mp0) cc_final: 0.8509 (mp0) outliers start: 25 outliers final: 12 residues processed: 128 average time/residue: 0.0939 time to fit residues: 15.7297 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 : 0.302 ------------------------------------------------------------------------------- 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 351 VAL 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 870 VAL 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: 0.7980 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.064349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.055472 restraints weight = 23643.808| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.93 r_work: 0.2691 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8652 Z= 0.128 Angle : 0.515 6.534 11968 Z= 0.276 Chirality : 0.036 0.160 1360 Planarity : 0.003 0.037 1301 Dihedral : 17.339 178.380 1951 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.02 % Favored : 93.86 % Rotamer: Outliers : 2.67 % Allowed : 12.15 % Favored : 85.18 % 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: 0.52 (0.29), residues: 847 helix: 1.38 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.51 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 204 TYR 0.015 0.001 TYR A 708 PHE 0.010 0.001 PHE A 534 TRP 0.009 0.002 TRP A 423 HIS 0.005 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8652) covalent geometry : angle 0.51484 (11968) hydrogen bonds : bond 0.04325 ( 430) hydrogen bonds : angle 4.17953 ( 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 112 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7252 (ptpt) REVERT: A 407 ASN cc_start: 0.8322 (t0) cc_final: 0.7929 (t0) REVERT: A 469 MET cc_start: 0.8911 (mmp) cc_final: 0.8615 (mmp) REVERT: A 676 MET cc_start: 0.8342 (tpt) cc_final: 0.8012 (tpt) REVERT: A 900 TYR cc_start: 0.8556 (t80) cc_final: 0.8226 (t80) REVERT: A 952 GLU cc_start: 0.8876 (mp0) cc_final: 0.8521 (mp0) outliers start: 20 outliers final: 10 residues processed: 110 average time/residue: 0.1059 time to fit residues: 15.0242 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 : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LYS 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 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: 3.9990 chunk 15 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN A 431 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.058444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.049979 restraints weight = 24105.157| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 1.85 r_work: 0.2553 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.4325 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= 0.242 Angle : 0.633 8.076 11968 Z= 0.341 Chirality : 0.041 0.169 1360 Planarity : 0.004 0.037 1301 Dihedral : 17.551 179.854 1951 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.44 % Favored : 92.44 % Rotamer: Outliers : 2.94 % Allowed : 13.22 % Favored : 83.85 % 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: 0.24 (0.28), residues: 847 helix: 1.18 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.67 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 218 TYR 0.019 0.002 TYR A 708 PHE 0.018 0.002 PHE A 857 TRP 0.008 0.003 TRP A 241 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00546 ( 8652) covalent geometry : angle 0.63344 (11968) hydrogen bonds : bond 0.05399 ( 430) hydrogen bonds : angle 4.42471 ( 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 112 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7298 (ptpt) REVERT: A 407 ASN cc_start: 0.8370 (t0) cc_final: 0.8081 (t0) REVERT: A 456 LEU cc_start: 0.2369 (OUTLIER) cc_final: 0.2123 (mm) REVERT: A 676 MET cc_start: 0.8724 (tpt) cc_final: 0.8468 (tpt) REVERT: A 803 ASN cc_start: 0.6642 (t0) cc_final: 0.6386 (t0) REVERT: A 952 GLU cc_start: 0.8933 (mp0) cc_final: 0.8619 (mp0) outliers start: 22 outliers final: 10 residues processed: 108 average time/residue: 0.0983 time to fit residues: 13.7027 Evaluate side-chains 96 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 302 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 790 ILE 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: 0.0000 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** 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 = 0.2905 r_free = 0.2905 target = 0.059617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.051168 restraints weight = 23924.644| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 1.89 r_work: 0.2583 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.4346 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= 0.164 Angle : 0.576 7.238 11968 Z= 0.309 Chirality : 0.038 0.162 1360 Planarity : 0.004 0.038 1301 Dihedral : 17.488 178.114 1949 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.85 % Favored : 93.03 % Rotamer: Outliers : 2.54 % Allowed : 14.15 % Favored : 83.31 % 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: 0.37 (0.29), residues: 847 helix: 1.20 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.51 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 218 TYR 0.015 0.002 TYR A 708 PHE 0.011 0.001 PHE A 534 TRP 0.010 0.002 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8652) covalent geometry : angle 0.57555 (11968) hydrogen bonds : bond 0.04631 ( 430) hydrogen bonds : angle 4.32513 ( 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 104 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6368 (tt0) REVERT: A 358 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7245 (ptpt) REVERT: A 407 ASN cc_start: 0.8417 (t0) cc_final: 0.8181 (t0) REVERT: A 676 MET cc_start: 0.8661 (tpt) cc_final: 0.8418 (tpt) REVERT: A 806 LYS cc_start: 0.8976 (tptp) cc_final: 0.8691 (tptt) REVERT: A 814 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6763 (mm-30) REVERT: A 952 GLU cc_start: 0.8903 (mp0) cc_final: 0.8592 (mp0) outliers start: 19 outliers final: 12 residues processed: 101 average time/residue: 0.0971 time to fit residues: 12.7119 Evaluate side-chains 98 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 94 GLN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 456 LEU 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 947 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2934 r_free = 0.2934 target = 0.060810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.052387 restraints weight = 23874.368| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 1.88 r_work: 0.2616 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8652 Z= 0.132 Angle : 0.540 6.920 11968 Z= 0.290 Chirality : 0.036 0.157 1360 Planarity : 0.003 0.038 1301 Dihedral : 17.454 178.286 1949 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.97 % Favored : 92.92 % Rotamer: Outliers : 2.67 % Allowed : 14.42 % Favored : 82.91 % 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: 0.55 (0.29), residues: 847 helix: 1.36 (0.23), residues: 540 sheet: None (None), residues: 0 loop : -1.47 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.015 0.001 TYR A 708 PHE 0.010 0.001 PHE A 534 TRP 0.005 0.001 TRP A 241 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8652) covalent geometry : angle 0.54010 (11968) hydrogen bonds : bond 0.04239 ( 430) hydrogen bonds : angle 4.22890 ( 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: 20 poor density : 90 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6375 (tt0) REVERT: A 358 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7231 (ptpt) REVERT: A 407 ASN cc_start: 0.8533 (t0) cc_final: 0.8088 (t0) REVERT: A 676 MET cc_start: 0.8516 (tpt) cc_final: 0.8225 (tpt) REVERT: A 814 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6685 (mm-30) REVERT: A 952 GLU cc_start: 0.8885 (mp0) cc_final: 0.8578 (mp0) outliers start: 20 outliers final: 9 residues processed: 104 average time/residue: 0.0959 time to fit residues: 13.1675 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 : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 456 LEU 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 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: 1.9990 chunk 83 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 80 optimal weight: 0.0060 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2950 r_free = 0.2950 target = 0.061509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.053040 restraints weight = 24058.880| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 1.88 r_work: 0.2633 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8652 Z= 0.125 Angle : 0.547 8.720 11968 Z= 0.292 Chirality : 0.036 0.155 1360 Planarity : 0.003 0.039 1301 Dihedral : 17.432 178.119 1949 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.49 % Favored : 93.39 % Rotamer: Outliers : 2.27 % Allowed : 15.22 % 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: 0.60 (0.29), residues: 847 helix: 1.38 (0.23), residues: 540 sheet: None (None), residues: 0 loop : -1.42 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 218 TYR 0.015 0.001 TYR A 708 PHE 0.009 0.001 PHE A 534 TRP 0.004 0.001 TRP A 241 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8652) covalent geometry : angle 0.54694 (11968) hydrogen bonds : bond 0.04090 ( 430) hydrogen bonds : angle 4.17385 ( 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 107 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6316 (tt0) REVERT: A 358 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7147 (ptpt) REVERT: A 407 ASN cc_start: 0.8493 (t0) cc_final: 0.8035 (t0) REVERT: A 676 MET cc_start: 0.8440 (tpt) cc_final: 0.8136 (tpt) REVERT: A 775 ARG cc_start: 0.6037 (mmp80) cc_final: 0.5655 (mmp80) REVERT: A 814 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6711 (mm-30) REVERT: A 952 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8582 (mp0) outliers start: 17 outliers final: 13 residues processed: 103 average time/residue: 0.0977 time to fit residues: 13.0362 Evaluate side-chains 103 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 456 LEU 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: 0.3980 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 0.0870 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.061152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.052663 restraints weight = 23994.439| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 1.89 r_work: 0.2624 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.4369 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= 0.135 Angle : 0.562 7.945 11968 Z= 0.300 Chirality : 0.036 0.155 1360 Planarity : 0.003 0.039 1301 Dihedral : 17.433 178.316 1949 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.08 % Favored : 92.80 % Rotamer: Outliers : 2.27 % Allowed : 15.09 % Favored : 82.64 % 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: 0.63 (0.29), residues: 847 helix: 1.42 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.36 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 218 TYR 0.015 0.001 TYR A 708 PHE 0.010 0.001 PHE A 534 TRP 0.005 0.001 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8652) covalent geometry : angle 0.56197 (11968) hydrogen bonds : bond 0.04177 ( 430) hydrogen bonds : angle 4.21844 ( 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: 17 poor density : 89 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.6465 (pm20) cc_final: 0.6158 (pp20) REVERT: A 334 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6251 (tt0) REVERT: A 358 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7172 (ptpt) REVERT: A 474 MET cc_start: 0.8772 (mtt) cc_final: 0.8486 (mtt) REVERT: A 676 MET cc_start: 0.8455 (tpt) cc_final: 0.8135 (tpt) REVERT: A 768 ASP cc_start: 0.8758 (t0) cc_final: 0.8541 (t0) REVERT: A 814 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6729 (mm-30) REVERT: A 952 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8577 (mp0) outliers start: 17 outliers final: 12 residues processed: 103 average time/residue: 0.0994 time to fit residues: 13.2040 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 : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 456 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.057333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.049090 restraints weight = 24419.606| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 1.86 r_work: 0.2531 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2426 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8652 Z= 0.225 Angle : 0.660 8.007 11968 Z= 0.351 Chirality : 0.040 0.169 1360 Planarity : 0.004 0.038 1301 Dihedral : 17.590 179.107 1949 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.91 % Favored : 91.97 % Rotamer: Outliers : 2.27 % Allowed : 15.89 % Favored : 81.84 % 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: 0.36 (0.29), residues: 847 helix: 1.19 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.44 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 218 TYR 0.017 0.002 TYR A 136 PHE 0.013 0.002 PHE A 857 TRP 0.008 0.002 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 8652) covalent geometry : angle 0.65953 (11968) hydrogen bonds : bond 0.05148 ( 430) hydrogen bonds : angle 4.43372 ( 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 106 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6463 (tt0) REVERT: A 358 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7249 (ptpt) REVERT: A 410 GLN cc_start: 0.8518 (pm20) cc_final: 0.8241 (pm20) REVERT: A 676 MET cc_start: 0.8702 (tpt) cc_final: 0.8396 (tpt) REVERT: A 776 LYS cc_start: 0.8386 (mtmm) cc_final: 0.7920 (mtmt) REVERT: A 814 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6931 (mm-30) REVERT: A 952 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8661 (mp0) outliers start: 17 outliers final: 13 residues processed: 105 average time/residue: 0.1063 time to fit residues: 14.4290 Evaluate side-chains 103 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 302 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 456 LEU 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 778 VAL 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: 0.6980 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2883 r_free = 0.2883 target = 0.058759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.050477 restraints weight = 24023.595| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 1.85 r_work: 0.2569 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8652 Z= 0.164 Angle : 0.642 10.732 11968 Z= 0.338 Chirality : 0.038 0.159 1360 Planarity : 0.004 0.038 1301 Dihedral : 17.546 178.077 1949 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.32 % Favored : 92.56 % Rotamer: Outliers : 1.74 % Allowed : 16.69 % 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: 0.45 (0.29), residues: 847 helix: 1.28 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.46 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 218 TYR 0.015 0.002 TYR A 79 PHE 0.010 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 covalent geometry : bond 0.00367 ( 8652) covalent geometry : angle 0.64234 (11968) hydrogen bonds : bond 0.04589 ( 430) hydrogen bonds : angle 4.40513 ( 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 104 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6394 (tt0) REVERT: A 358 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7241 (ptpt) REVERT: A 676 MET cc_start: 0.8652 (tpt) cc_final: 0.8361 (tpt) REVERT: A 776 LYS cc_start: 0.8352 (mtmm) cc_final: 0.7936 (mtmt) REVERT: A 814 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6884 (mm-30) REVERT: A 891 MET cc_start: 0.8799 (tpp) cc_final: 0.8584 (tpp) REVERT: A 952 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8601 (mp0) outliers start: 13 outliers final: 10 residues processed: 102 average time/residue: 0.1085 time to fit residues: 14.3670 Evaluate side-chains 100 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 456 LEU 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: 0.9980 chunk 75 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.058975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.050661 restraints weight = 24252.328| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 1.87 r_work: 0.2576 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8652 Z= 0.159 Angle : 0.635 11.244 11968 Z= 0.334 Chirality : 0.038 0.157 1360 Planarity : 0.004 0.039 1301 Dihedral : 17.534 178.369 1949 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.56 % Favored : 92.33 % 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: 0.47 (0.29), residues: 847 helix: 1.30 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.46 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 218 TYR 0.016 0.002 TYR A 79 PHE 0.010 0.001 PHE A 196 TRP 0.007 0.002 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8652) covalent geometry : angle 0.63507 (11968) hydrogen bonds : bond 0.04492 ( 430) hydrogen bonds : angle 4.39478 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1603.78 seconds wall clock time: 28 minutes 14.79 seconds (1694.79 seconds total)