Starting phenix.real_space_refine on Fri Jul 3 01:55:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yoj_33983/07_2026/7yoj_33983.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yoj_33983/07_2026/7yoj_33983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7yoj_33983/07_2026/7yoj_33983.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yoj_33983/07_2026/7yoj_33983.cif" model { file = "/net/cci-nas-00/data/ceres_data/7yoj_33983/07_2026/7yoj_33983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yoj_33983/07_2026/7yoj_33983.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yoj_33983/07_2026/7yoj_33983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yoj_33983/07_2026/7yoj_33983.map" } resolution = 3.36 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= 0.005 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 216 5.49 5 S 24 5.16 5 C 6436 2.51 5 N 2166 2.21 5 O 2703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 11545 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6947 Classifications: {'peptide': 867} Link IDs: {'PTRANS': 50, 'TRANS': 816} Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 248 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 612 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "B" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 3738 Classifications: {'RNA': 174} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 90, 'rna3p_pyr': 64} Link IDs: {'rna2p': 20, 'rna3p': 153} Time building chain proxies: 3.24, per 1000 atoms: 0.28 Number of scatterers: 11545 At special positions: 0 Unit cell: (107.856, 110.424, 128.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 216 15.00 O 2703 8.00 N 2166 7.00 C 6436 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: 1.27 Conformation dependent library (CDL) restraints added in 413.4 milliseconds 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 43.8% alpha, 9.1% beta 72 base pairs and 127 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 1 through 40 Processing helix chain 'A' and resid 48 through 70 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 170 through 183 removed outlier: 3.615A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 197 Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.822A pdb=" N TRP A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.626A pdb=" N LEU A 224 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 225' Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 234 through 260 removed outlier: 3.548A pdb=" N THR A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 287 Processing helix chain 'A' and resid 320 through 334 removed outlier: 3.817A pdb=" N VAL A 324 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 removed outlier: 4.183A pdb=" N PHE A 340 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 366 Processing helix chain 'A' and resid 431 through 436 removed outlier: 4.524A pdb=" N ASP A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 431 through 436' Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.561A pdb=" N GLY A 444 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 445' Processing helix chain 'A' and resid 457 through 468 Processing helix chain 'A' and resid 565 through 589 removed outlier: 3.575A pdb=" N ASN A 588 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 Processing helix chain 'A' and resid 615 through 633 Processing helix chain 'A' and resid 659 through 674 removed outlier: 3.771A pdb=" N LYS A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.571A pdb=" N VAL A 698 " --> pdb=" O THR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 717 Processing helix chain 'A' and resid 795 through 814 Proline residue: A 807 - end of helix Processing helix chain 'A' and resid 818 through 830 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 861 through 866 Processing sheet with id=AA1, first strand: chain 'A' and resid 383 through 385 removed outlier: 3.531A pdb=" N ARG A 502 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU A 503 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU A 147 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 450 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A 452 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 454 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU A 407 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 292 Processing sheet with id=AA3, first strand: chain 'A' and resid 481 through 486 removed outlier: 5.289A pdb=" N HIS A 483 " --> pdb=" O LYS A 510 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS A 510 " --> pdb=" O HIS A 483 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 485 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 687 through 690 removed outlier: 7.608A pdb=" N VAL A 641 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE A 534 " --> pdb=" O VAL A 641 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ALA A 643 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE A 536 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 535 " --> pdb=" O ALA A 547 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 548 " --> pdb=" O ILE A 557 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 739 through 740 removed outlier: 3.573A pdb=" N GLY A 854 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 858 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 841 " --> pdb=" O ILE A 858 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 792 " --> pdb=" O TYR A 842 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 781 through 782 302 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 192 hydrogen bonds 372 hydrogen bond angles 0 basepair planarities 72 basepair parallelities 127 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1520 1.32 - 1.45: 4485 1.45 - 1.57: 5779 1.57 - 1.69: 429 1.69 - 1.82: 35 Bond restraints: 12248 Sorted by residual: bond pdb=" C1' DC D 6 " pdb=" N1 DC D 6 " ideal model delta sigma weight residual 1.468 1.534 -0.066 1.40e-02 5.10e+03 2.21e+01 bond pdb=" C PRO A 114 " pdb=" O PRO A 114 " ideal model delta sigma weight residual 1.240 1.197 0.044 1.12e-02 7.97e+03 1.53e+01 bond pdb=" C1' DT D 12 " pdb=" N1 DT D 12 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.26e+01 bond pdb=" C3' DC D 18 " pdb=" C2' DC D 18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DT D 14 " pdb=" C2' DT D 14 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.31e+00 ... (remaining 12243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 16865 2.07 - 4.13: 632 4.13 - 6.20: 66 6.20 - 8.27: 17 8.27 - 10.33: 10 Bond angle restraints: 17590 Sorted by residual: angle pdb=" O3' G B 155 " pdb=" C3' G B 155 " pdb=" C2' G B 155 " ideal model delta sigma weight residual 109.50 119.83 -10.33 1.50e+00 4.44e-01 4.74e+01 angle pdb=" CA PRO A 862 " pdb=" N PRO A 862 " pdb=" CD PRO A 862 " ideal model delta sigma weight residual 112.00 105.22 6.78 1.40e+00 5.10e-01 2.35e+01 angle pdb=" O4' DG D 9 " pdb=" C4' DG D 9 " pdb=" C3' DG D 9 " ideal model delta sigma weight residual 106.00 103.38 2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT D 12 " pdb=" C4 DT D 12 " pdb=" O4 DT D 12 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT C 6 " pdb=" C4 DT C 6 " pdb=" O4 DT C 6 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 17585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.61: 6333 34.61 - 69.23: 502 69.23 - 103.84: 44 103.84 - 138.45: 4 138.45 - 173.07: 4 Dihedral angle restraints: 6887 sinusoidal: 4378 harmonic: 2509 Sorted by residual: dihedral pdb=" O4' U B 26 " pdb=" C1' U B 26 " pdb=" N1 U B 26 " pdb=" C2 U B 26 " ideal model delta sinusoidal sigma weight residual -160.00 -0.88 -159.12 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' U B 148 " pdb=" C1' U B 148 " pdb=" N1 U B 148 " pdb=" C2 U B 148 " ideal model delta sinusoidal sigma weight residual -160.00 -18.27 -141.73 1 1.50e+01 4.44e-03 7.62e+01 dihedral pdb=" O4' C B 66 " pdb=" C1' C B 66 " pdb=" N1 C B 66 " pdb=" C2 C B 66 " ideal model delta sinusoidal sigma weight residual -160.00 -70.12 -89.88 1 1.50e+01 4.44e-03 4.26e+01 ... (remaining 6884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1841 0.085 - 0.169: 180 0.169 - 0.254: 24 0.254 - 0.338: 2 0.338 - 0.423: 3 Chirality restraints: 2050 Sorted by residual: chirality pdb=" P U B 99 " pdb=" OP1 U B 99 " pdb=" OP2 U B 99 " pdb=" O5' U B 99 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C3' G B 155 " pdb=" C4' G B 155 " pdb=" O3' G B 155 " pdb=" C2' G B 155 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CG LEU A 50 " pdb=" CB LEU A 50 " pdb=" CD1 LEU A 50 " pdb=" CD2 LEU A 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 2047 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 861 " 0.091 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO A 862 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO A 862 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 862 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 71 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" CG ASP A 71 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP A 71 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP A 71 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 143 " 0.038 5.00e-02 4.00e+02 5.69e-02 5.19e+00 pdb=" N PRO A 144 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " 0.032 5.00e-02 4.00e+02 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3217 2.82 - 3.34: 10218 3.34 - 3.86: 23012 3.86 - 4.38: 25418 4.38 - 4.90: 36931 Nonbonded interactions: 98796 Sorted by model distance: nonbonded pdb=" OH TYR A 730 " pdb=" O ARG A 852 " model vdw 2.304 3.040 nonbonded pdb=" O2' G B 153 " pdb=" OP1 G B 155 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR A 544 " pdb=" OG SER A 621 " model vdw 2.316 3.040 nonbonded pdb=" O SER A 771 " pdb=" OG SER A 771 " model vdw 2.321 3.040 nonbonded pdb=" O SER A 757 " pdb=" OG SER A 757 " model vdw 2.327 3.040 ... (remaining 98791 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.220 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 : 0.005 0.072 12248 Z= 0.329 Angle : 0.886 10.333 17590 Z= 0.526 Chirality : 0.055 0.423 2050 Planarity : 0.007 0.135 1474 Dihedral : 20.761 173.068 5265 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.90 % Favored : 93.64 % Rotamer: Outliers : 2.19 % Allowed : 24.73 % Favored : 73.09 % 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: -2.03 (0.25), residues: 865 helix: -0.88 (0.24), residues: 336 sheet: -1.83 (0.60), residues: 71 loop : -1.59 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 390 TYR 0.024 0.002 TYR A 21 PHE 0.026 0.002 PHE A 384 TRP 0.019 0.002 TRP A 244 HIS 0.018 0.002 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.33 (12248) covalent geometry : angle 0.88646 / 0.53 (17590) hydrogen bonds : bond 0.15085 / 10.73 ( 494) hydrogen bonds : angle 7.14203 / 5.17 ( 1251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8029 (t80) cc_final: 0.7745 (t80) REVERT: A 104 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6324 (mp0) outliers start: 16 outliers final: 8 residues processed: 81 average time/residue: 0.1038 time to fit residues: 11.7122 Evaluate side-chains 66 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 858 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 38 optimal weight: 0.0370 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 458 HIS A 670 GLN A 830 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.160154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.116574 restraints weight = 26915.593| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.33 r_work: 0.3561 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12248 Z= 0.172 Angle : 0.673 7.098 17590 Z= 0.347 Chirality : 0.039 0.294 2050 Planarity : 0.006 0.087 1474 Dihedral : 19.366 174.036 3520 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.51 % Favored : 95.38 % Rotamer: Outliers : 2.32 % Allowed : 25.41 % Favored : 72.27 % 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: -1.02 (0.28), residues: 865 helix: 0.35 (0.27), residues: 340 sheet: -1.67 (0.51), residues: 89 loop : -1.27 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 390 TYR 0.014 0.001 TYR A 21 PHE 0.020 0.002 PHE A 384 TRP 0.012 0.001 TRP A 244 HIS 0.011 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (12248) covalent geometry : angle 0.67323 / 0.35 (17590) hydrogen bonds : bond 0.05545 / 3.63 ( 494) hydrogen bonds : angle 4.62536 / 3.32 ( 1251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 ARG cc_start: 0.7900 (ptm160) cc_final: 0.7653 (ptt180) outliers start: 17 outliers final: 13 residues processed: 74 average time/residue: 0.1140 time to fit residues: 11.7217 Evaluate side-chains 68 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 858 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 18 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 66 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.156285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.110851 restraints weight = 27243.337| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.76 r_work: 0.3441 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 12248 Z= 0.252 Angle : 0.709 8.519 17590 Z= 0.368 Chirality : 0.041 0.316 2050 Planarity : 0.005 0.069 1474 Dihedral : 19.367 171.451 3512 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.90 % Favored : 93.99 % Rotamer: Outliers : 3.14 % Allowed : 24.73 % Favored : 72.13 % 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: -0.61 (0.29), residues: 865 helix: 0.89 (0.28), residues: 343 sheet: -2.05 (0.50), residues: 96 loop : -1.04 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 605 TYR 0.011 0.002 TYR A 426 PHE 0.032 0.002 PHE A 384 TRP 0.012 0.002 TRP A 378 HIS 0.011 0.002 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.25 (12248) covalent geometry : angle 0.70939 / 0.37 (17590) hydrogen bonds : bond 0.05396 / 3.42 ( 494) hydrogen bonds : angle 4.34961 / 3.14 ( 1251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8416 (t0) cc_final: 0.8090 (t0) REVERT: A 290 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6047 (pp) REVERT: A 334 MET cc_start: 0.8022 (ptt) cc_final: 0.7808 (ptp) REVERT: A 563 ASP cc_start: 0.7965 (p0) cc_final: 0.7527 (p0) REVERT: A 704 TRP cc_start: 0.7831 (t60) cc_final: 0.7560 (t60) REVERT: A 706 LYS cc_start: 0.7835 (mttp) cc_final: 0.7521 (mtpp) outliers start: 23 outliers final: 21 residues processed: 80 average time/residue: 0.0984 time to fit residues: 11.2342 Evaluate side-chains 75 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 20 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 ASN A 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.157417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.108561 restraints weight = 27108.014| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.69 r_work: 0.3498 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12248 Z= 0.170 Angle : 0.640 10.937 17590 Z= 0.330 Chirality : 0.038 0.242 2050 Planarity : 0.005 0.058 1474 Dihedral : 19.356 168.138 3512 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.51 % Favored : 95.38 % Rotamer: Outliers : 3.96 % Allowed : 23.77 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.29), residues: 865 helix: 1.14 (0.28), residues: 342 sheet: -2.03 (0.50), residues: 96 loop : -0.95 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 605 TYR 0.014 0.001 TYR A 426 PHE 0.018 0.002 PHE A 384 TRP 0.017 0.001 TRP A 244 HIS 0.009 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (12248) covalent geometry : angle 0.63987 / 0.33 (17590) hydrogen bonds : bond 0.04534 / 2.89 ( 494) hydrogen bonds : angle 4.16431 / 2.99 ( 1251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8372 (t0) cc_final: 0.8075 (t0) REVERT: A 290 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.5930 (pp) REVERT: A 351 MET cc_start: 0.7698 (mtm) cc_final: 0.7439 (mtp) outliers start: 29 outliers final: 20 residues processed: 84 average time/residue: 0.1040 time to fit residues: 12.3702 Evaluate side-chains 75 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 858 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 82 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 0.0570 chunk 102 optimal weight: 40.0000 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 97 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 overall best weight: 1.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS A 215 ASN A 246 GLN ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.157544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.108888 restraints weight = 27047.221| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.70 r_work: 0.3503 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12248 Z= 0.161 Angle : 0.629 9.544 17590 Z= 0.326 Chirality : 0.038 0.294 2050 Planarity : 0.005 0.058 1474 Dihedral : 19.326 168.932 3512 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.09 % Favored : 94.80 % Rotamer: Outliers : 4.78 % Allowed : 23.22 % Favored : 71.99 % 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: -0.14 (0.30), residues: 865 helix: 1.35 (0.28), residues: 342 sheet: -1.95 (0.51), residues: 96 loop : -0.80 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 749 TYR 0.011 0.001 TYR A 426 PHE 0.034 0.002 PHE A 165 TRP 0.019 0.001 TRP A 244 HIS 0.010 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (12248) covalent geometry : angle 0.62907 / 0.33 (17590) hydrogen bonds : bond 0.04365 / 2.76 ( 494) hydrogen bonds : angle 4.06620 / 2.94 ( 1251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 58 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8379 (t0) cc_final: 0.8063 (t0) REVERT: A 290 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6007 (pp) REVERT: A 351 MET cc_start: 0.7808 (mtm) cc_final: 0.7536 (mtp) REVERT: A 860 LEU cc_start: 0.8504 (mm) cc_final: 0.8217 (mp) outliers start: 35 outliers final: 23 residues processed: 85 average time/residue: 0.0945 time to fit residues: 11.4144 Evaluate side-chains 77 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 833 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 25 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 ASN A 246 GLN ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** 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 = 0.4410 r_free = 0.4410 target = 0.158542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.109920 restraints weight = 27174.214| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.71 r_work: 0.3520 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12248 Z= 0.143 Angle : 0.606 9.254 17590 Z= 0.314 Chirality : 0.037 0.231 2050 Planarity : 0.004 0.045 1474 Dihedral : 19.265 168.081 3510 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.72 % Rotamer: Outliers : 3.69 % Allowed : 24.32 % Favored : 71.99 % 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: 0.02 (0.30), residues: 865 helix: 1.52 (0.28), residues: 342 sheet: -1.89 (0.51), residues: 96 loop : -0.75 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 371 TYR 0.011 0.001 TYR A 426 PHE 0.019 0.002 PHE A 165 TRP 0.014 0.001 TRP A 244 HIS 0.008 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (12248) covalent geometry : angle 0.60586 / 0.31 (17590) hydrogen bonds : bond 0.04094 / 2.60 ( 494) hydrogen bonds : angle 3.96367 / 2.86 ( 1251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8404 (t0) cc_final: 0.8118 (t0) REVERT: A 290 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6112 (pp) REVERT: A 860 LEU cc_start: 0.8527 (mm) cc_final: 0.8247 (mp) outliers start: 27 outliers final: 20 residues processed: 81 average time/residue: 0.1045 time to fit residues: 11.9457 Evaluate side-chains 74 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 833 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 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 = 0.4423 r_free = 0.4423 target = 0.159722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.111274 restraints weight = 27039.593| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.72 r_work: 0.3542 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12248 Z= 0.126 Angle : 0.610 12.561 17590 Z= 0.312 Chirality : 0.037 0.293 2050 Planarity : 0.004 0.042 1474 Dihedral : 19.212 168.099 3510 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.62 % Favored : 95.26 % Rotamer: Outliers : 2.87 % Allowed : 25.55 % Favored : 71.58 % 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: 0.10 (0.30), residues: 865 helix: 1.63 (0.28), residues: 339 sheet: -1.81 (0.51), residues: 96 loop : -0.73 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 371 TYR 0.011 0.001 TYR A 426 PHE 0.016 0.002 PHE A 801 TRP 0.023 0.001 TRP A 704 HIS 0.009 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (12248) covalent geometry : angle 0.60964 / 0.31 (17590) hydrogen bonds : bond 0.03944 / 2.52 ( 494) hydrogen bonds : angle 3.89197 / 2.83 ( 1251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8384 (t0) cc_final: 0.8098 (t0) REVERT: A 290 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6131 (pp) REVERT: A 304 HIS cc_start: 0.6786 (t-170) cc_final: 0.6379 (t-170) REVERT: A 860 LEU cc_start: 0.8506 (mm) cc_final: 0.8243 (mp) outliers start: 21 outliers final: 17 residues processed: 73 average time/residue: 0.1174 time to fit residues: 12.1424 Evaluate side-chains 71 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 833 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 102 optimal weight: 40.0000 chunk 49 optimal weight: 0.0370 chunk 104 optimal weight: 10.0000 chunk 67 optimal weight: 0.3980 chunk 29 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 103 optimal weight: 40.0000 chunk 13 optimal weight: 7.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 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 = 0.4429 r_free = 0.4429 target = 0.160442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.112691 restraints weight = 27014.683| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.69 r_work: 0.3560 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12248 Z= 0.123 Angle : 0.603 8.550 17590 Z= 0.308 Chirality : 0.036 0.217 2050 Planarity : 0.004 0.040 1474 Dihedral : 19.101 168.783 3510 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.39 % Favored : 95.49 % Rotamer: Outliers : 3.01 % Allowed : 25.82 % Favored : 71.17 % 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: 0.26 (0.30), residues: 865 helix: 1.77 (0.28), residues: 340 sheet: -1.49 (0.53), residues: 94 loop : -0.73 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 39 TYR 0.010 0.001 TYR A 426 PHE 0.018 0.001 PHE A 165 TRP 0.020 0.001 TRP A 704 HIS 0.008 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (12248) covalent geometry : angle 0.60283 / 0.31 (17590) hydrogen bonds : bond 0.03813 / 2.45 ( 494) hydrogen bonds : angle 3.79293 / 2.75 ( 1251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8379 (t0) cc_final: 0.8092 (t0) REVERT: A 290 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6033 (pp) REVERT: A 334 MET cc_start: 0.7571 (ptt) cc_final: 0.7219 (ptt) REVERT: A 860 LEU cc_start: 0.8494 (mm) cc_final: 0.8224 (mp) outliers start: 22 outliers final: 18 residues processed: 76 average time/residue: 0.1103 time to fit residues: 11.9231 Evaluate side-chains 68 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 833 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 chunk 103 optimal weight: 40.0000 chunk 42 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 86 optimal weight: 30.0000 chunk 92 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 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 = 0.4390 r_free = 0.4390 target = 0.157890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.108647 restraints weight = 26657.140| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.69 r_work: 0.3475 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12248 Z= 0.174 Angle : 0.625 8.801 17590 Z= 0.321 Chirality : 0.037 0.244 2050 Planarity : 0.004 0.042 1474 Dihedral : 19.082 170.015 3510 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.55 % Favored : 94.34 % Rotamer: Outliers : 3.55 % Allowed : 26.09 % Favored : 70.36 % 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: 0.21 (0.30), residues: 865 helix: 1.77 (0.28), residues: 341 sheet: -1.72 (0.52), residues: 96 loop : -0.74 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 107 TYR 0.007 0.001 TYR A 426 PHE 0.021 0.002 PHE A 384 TRP 0.015 0.001 TRP A 704 HIS 0.010 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (12248) covalent geometry : angle 0.62461 / 0.32 (17590) hydrogen bonds : bond 0.04095 / 2.62 ( 494) hydrogen bonds : angle 3.83922 / 2.79 ( 1251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8505 (t0) cc_final: 0.8219 (t0) REVERT: A 290 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6098 (pp) REVERT: A 860 LEU cc_start: 0.8576 (mm) cc_final: 0.8296 (mp) outliers start: 26 outliers final: 22 residues processed: 79 average time/residue: 0.0953 time to fit residues: 10.8741 Evaluate side-chains 77 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 833 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 102 optimal weight: 40.0000 chunk 23 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 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 = 0.4398 r_free = 0.4398 target = 0.158578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.109843 restraints weight = 26692.474| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.71 r_work: 0.3493 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12248 Z= 0.144 Angle : 0.614 8.445 17590 Z= 0.315 Chirality : 0.037 0.246 2050 Planarity : 0.004 0.043 1474 Dihedral : 19.097 168.741 3510 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.86 % Favored : 95.03 % Rotamer: Outliers : 3.01 % Allowed : 27.19 % Favored : 69.81 % 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: 0.18 (0.30), residues: 865 helix: 1.74 (0.28), residues: 339 sheet: -1.64 (0.53), residues: 96 loop : -0.76 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 12 TYR 0.010 0.001 TYR A 426 PHE 0.016 0.002 PHE A 801 TRP 0.015 0.001 TRP A 704 HIS 0.008 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (12248) covalent geometry : angle 0.61446 / 0.31 (17590) hydrogen bonds : bond 0.03979 / 2.56 ( 494) hydrogen bonds : angle 3.82760 / 2.77 ( 1251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8416 (t0) cc_final: 0.8143 (t0) REVERT: A 290 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6070 (pp) REVERT: A 334 MET cc_start: 0.7633 (ptt) cc_final: 0.7311 (ptt) REVERT: A 860 LEU cc_start: 0.8550 (mm) cc_final: 0.8288 (mp) outliers start: 22 outliers final: 21 residues processed: 71 average time/residue: 0.0963 time to fit residues: 10.0215 Evaluate side-chains 74 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 833 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 64 optimal weight: 0.0060 chunk 37 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 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 = 0.4405 r_free = 0.4405 target = 0.159382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.110691 restraints weight = 26831.615| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.72 r_work: 0.3508 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12248 Z= 0.131 Angle : 0.608 8.013 17590 Z= 0.310 Chirality : 0.036 0.218 2050 Planarity : 0.004 0.048 1474 Dihedral : 19.068 168.542 3510 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.74 % Favored : 95.14 % Rotamer: Outliers : 2.87 % Allowed : 27.05 % Favored : 70.08 % 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: 0.23 (0.30), residues: 865 helix: 1.78 (0.28), residues: 339 sheet: -1.51 (0.54), residues: 96 loop : -0.77 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 12 TYR 0.011 0.001 TYR A 426 PHE 0.016 0.001 PHE A 774 TRP 0.016 0.001 TRP A 704 HIS 0.008 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (12248) covalent geometry : angle 0.60837 / 0.31 (17590) hydrogen bonds : bond 0.03833 / 2.47 ( 494) hydrogen bonds : angle 3.78398 / 2.74 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2733.79 seconds wall clock time: 47 minutes 29.61 seconds (2849.61 seconds total)