Starting phenix.real_space_refine on Fri Sep 11 20:35:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yoj_33983/09_2026/7yoj_33983.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yoj_33983/09_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_33983/09_2026/7yoj_33983.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yoj_33983/09_2026/7yoj_33983.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yoj_33983/09_2026/7yoj_33983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yoj_33983/09_2026/7yoj_33983.map" model { file = "/net/cci-nas-00/data/ceres_data/7yoj_33983/09_2026/7yoj_33983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yoj_33983/09_2026/7yoj_33983.cif" } 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-2.2.1-6174/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: {'RNAv2': 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: 2.40, per 1000 atoms: 0.21 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: 0.89 Conformation dependent library (CDL) restraints added in 364.4 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: 1.55 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: 2.90 Time building geometry restraints manager: 1.22 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 - 2.01: 16424 2.01 - 4.03: 1019 4.03 - 6.04: 117 6.04 - 8.05: 20 8.05 - 10.07: 10 Bond angle restraints: 17590 Sorted by residual: 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=" C3' G B 133 " pdb=" O3' G B 133 " pdb=" P A B 134 " ideal model delta sigma weight residual 119.70 124.96 -5.26 1.20e+00 6.94e-01 1.92e+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: 6155 34.61 - 69.23: 687 69.23 - 103.84: 43 103.84 - 138.45: 0 138.45 - 173.07: 2 Dihedral angle restraints: 6887 sinusoidal: 4378 harmonic: 2509 Sorted by residual: dihedral pdb=" C4' U B 99 " pdb=" C3' U B 99 " pdb=" C2' U B 99 " pdb=" C1' U B 99 " ideal model delta sinusoidal sigma weight residual 36.34 -41.26 77.60 1 3.10e+00 1.04e-01 7.85e+02 dihedral pdb=" C4' C B 93 " pdb=" C3' C B 93 " pdb=" C2' C B 93 " pdb=" C1' C B 93 " ideal model delta sinusoidal sigma weight residual 36.34 -39.21 75.56 1 3.10e+00 1.04e-01 7.50e+02 dihedral pdb=" C4' A B 154 " pdb=" C3' A B 154 " pdb=" C2' A B 154 " pdb=" C1' A B 154 " ideal model delta sinusoidal sigma weight residual 36.34 -38.60 74.94 1 3.10e+00 1.04e-01 7.39e+02 ... (remaining 6884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 1772 0.132 - 0.264: 235 0.264 - 0.396: 35 0.396 - 0.528: 7 0.528 - 0.660: 1 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 2.17 -2.83 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" P G B 60 " pdb=" OP1 G B 60 " pdb=" OP2 G B 60 " pdb=" O5' G B 60 " both_signs ideal model delta sigma weight residual True 2.17 -2.67 -0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" P G B 7 " pdb=" OP1 G B 7 " pdb=" OP2 G B 7 " pdb=" O5' G B 7 " both_signs ideal model delta sigma weight residual True 2.17 -2.66 -0.48 2.00e-01 2.50e+01 5.87e+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: 0.930 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.570 Find NCS groups from input model: 0.040 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.810 ------------------------------------------------------------------------------- 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= 0.328 Angle : 1.014 10.068 17590 Z= 0.536 Chirality : 0.098 0.660 2050 Planarity : 0.007 0.135 1474 Dihedral : 22.478 173.068 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 0.00505 / 0.33 (12248) covalent geometry : angle 1.01405 / 0.54 (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 : 0.292 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: 0.1179 time to fit residues: 13.3652 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 : 0.317 ------------------------------------------------------------------------------- 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: 3.9990 chunk 106 optimal weight: 5.9990 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 830 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.158465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.113371 restraints weight = 26907.925| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.56 r_work: 0.3489 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12248 Z= 0.243 Angle : 1.237 23.341 17590 Z= 0.515 Chirality : 0.117 1.906 2050 Planarity : 0.006 0.086 1474 Dihedral : 19.943 179.409 3520 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.51 % Favored : 95.38 % Rotamer: Outliers : 2.46 % Allowed : 25.00 % Favored : 72.54 % 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: -0.96 (0.28), residues: 865 helix: 0.38 (0.27), residues: 341 sheet: -1.64 (0.51), residues: 89 loop : -1.22 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 390 TYR 0.014 0.001 TYR A 426 PHE 0.021 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 0.00473 / 0.24 (12248) covalent geometry : angle 1.23653 / 0.51 (17590) hydrogen bonds : bond 0.05553 / 3.68 ( 494) hydrogen bonds : angle 4.62942 / 3.33 ( 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 82 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8444 (mt-10) REVERT: A 290 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.5867 (pp) REVERT: A 601 ARG cc_start: 0.7903 (ptm160) cc_final: 0.7675 (ptt180) outliers start: 18 outliers final: 13 residues processed: 78 average time/residue: 0.1272 time to fit residues: 13.8865 Evaluate side-chains 69 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 290 LEU 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: 3.9990 chunk 43 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 66 optimal weight: 1.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 670 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.153230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.102356 restraints weight = 26696.765| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.73 r_work: 0.3389 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12248 Z= 0.227 Angle : 1.023 16.879 17590 Z= 0.439 Chirality : 0.076 0.846 2050 Planarity : 0.005 0.069 1474 Dihedral : 19.555 164.701 3512 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.32 % Favored : 94.57 % Rotamer: Outliers : 2.87 % Allowed : 24.45 % Favored : 72.68 % 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: -0.46 (0.29), residues: 865 helix: 0.97 (0.28), residues: 344 sheet: -1.87 (0.50), residues: 94 loop : -0.96 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 605 TYR 0.011 0.001 TYR A 426 PHE 0.026 0.002 PHE A 384 TRP 0.010 0.001 TRP A 244 HIS 0.010 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.23 (12248) covalent geometry : angle 1.02308 / 0.44 (17590) hydrogen bonds : bond 0.05541 / 3.65 ( 494) hydrogen bonds : angle 4.33477 / 3.13 ( 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 78 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8500 (t0) cc_final: 0.8155 (t0) REVERT: A 334 MET cc_start: 0.7973 (ptt) cc_final: 0.7771 (ptp) REVERT: A 601 ARG cc_start: 0.7963 (ptm160) cc_final: 0.7746 (ptt180) outliers start: 21 outliers final: 19 residues processed: 74 average time/residue: 0.1221 time to fit residues: 12.8316 Evaluate side-chains 67 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 250 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 276 SER 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 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: 7.9990 chunk 0 optimal weight: 40.0000 chunk 20 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 0.0980 chunk 23 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 HIS A 215 ASN ** 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 = 0.4330 r_free = 0.4330 target = 0.154085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.107617 restraints weight = 26895.158| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.55 r_work: 0.3410 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12248 Z= 0.227 Angle : 0.970 11.719 17590 Z= 0.417 Chirality : 0.067 0.521 2050 Planarity : 0.005 0.058 1474 Dihedral : 19.327 170.747 3512 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.86 % Favored : 95.03 % Rotamer: Outliers : 4.37 % Allowed : 23.36 % 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: -0.37 (0.29), residues: 865 helix: 1.17 (0.28), residues: 343 sheet: -2.00 (0.50), residues: 96 loop : -0.96 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 605 TYR 0.014 0.001 TYR A 426 PHE 0.026 0.002 PHE A 384 TRP 0.020 0.002 TRP A 704 HIS 0.009 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 (12248) covalent geometry : angle 0.96968 / 0.42 (17590) hydrogen bonds : bond 0.04942 / 3.22 ( 494) hydrogen bonds : angle 4.18820 / 3.02 ( 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 87 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8499 (t0) cc_final: 0.8165 (t0) REVERT: A 290 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6067 (pp) REVERT: A 351 MET cc_start: 0.7712 (mtm) cc_final: 0.7445 (mtp) outliers start: 32 outliers final: 22 residues processed: 82 average time/residue: 0.1185 time to fit residues: 13.8027 Evaluate side-chains 74 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 87 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR 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 387 THR Chi-restraints excluded: chain A residue 397 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 82 optimal weight: 0.0020 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 102 optimal weight: 30.0000 chunk 22 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 ASN ** A 335 GLN ** 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 = 0.4385 r_free = 0.4385 target = 0.157493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.108614 restraints weight = 26980.501| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.71 r_work: 0.3473 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2537 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= 0.149 Angle : 0.889 11.385 17590 Z= 0.383 Chirality : 0.062 0.439 2050 Planarity : 0.005 0.072 1474 Dihedral : 19.165 175.807 3506 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.05 % Favored : 95.84 % Rotamer: Outliers : 3.01 % Allowed : 25.14 % Favored : 71.86 % 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: -0.07 (0.30), residues: 865 helix: 1.40 (0.28), residues: 342 sheet: -1.87 (0.50), residues: 96 loop : -0.76 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 581 TYR 0.013 0.001 TYR A 426 PHE 0.030 0.002 PHE A 165 TRP 0.020 0.001 TRP A 704 HIS 0.009 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (12248) covalent geometry : angle 0.88940 / 0.38 (17590) hydrogen bonds : bond 0.04435 / 2.88 ( 494) hydrogen bonds : angle 4.02930 / 2.91 ( 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 79 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8482 (t0) cc_final: 0.8151 (t0) REVERT: A 290 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6173 (pp) REVERT: A 459 ASP cc_start: 0.8543 (m-30) cc_final: 0.8316 (m-30) REVERT: A 704 TRP cc_start: 0.8013 (t60) cc_final: 0.7630 (t60) REVERT: A 860 LEU cc_start: 0.8514 (mm) cc_final: 0.8240 (mp) outliers start: 22 outliers final: 16 residues processed: 74 average time/residue: 0.1062 time to fit residues: 11.6972 Evaluate side-chains 72 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 100 THR 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 276 SER Chi-restraints excluded: chain A residue 290 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 3 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 83 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 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 = 0.4397 r_free = 0.4397 target = 0.158491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.109509 restraints weight = 27169.648| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.72 r_work: 0.3490 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2652 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= 0.139 Angle : 0.868 10.551 17590 Z= 0.372 Chirality : 0.061 0.409 2050 Planarity : 0.004 0.046 1474 Dihedral : 19.009 177.841 3506 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 2.87 % Allowed : 25.27 % Favored : 71.86 % 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: 0.09 (0.30), residues: 865 helix: 1.58 (0.28), residues: 341 sheet: -1.64 (0.51), residues: 94 loop : -0.76 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 605 TYR 0.010 0.001 TYR A 426 PHE 0.016 0.002 PHE A 165 TRP 0.012 0.001 TRP A 244 HIS 0.009 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (12248) covalent geometry : angle 0.86806 / 0.37 (17590) hydrogen bonds : bond 0.04253 / 2.73 ( 494) hydrogen bonds : angle 3.92058 / 2.84 ( 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 82 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8462 (t0) cc_final: 0.8159 (t0) REVERT: A 290 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6229 (pp) REVERT: A 704 TRP cc_start: 0.8068 (t60) cc_final: 0.7702 (t60) REVERT: A 860 LEU cc_start: 0.8476 (mm) cc_final: 0.8203 (mp) outliers start: 21 outliers final: 14 residues processed: 76 average time/residue: 0.1112 time to fit residues: 12.3566 Evaluate side-chains 68 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 100 THR 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 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 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: 1.9990 chunk 60 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 72 optimal weight: 0.0270 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN ** A 335 GLN ** 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 = 0.4362 r_free = 0.4362 target = 0.158222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.110645 restraints weight = 26582.993| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.74 r_work: 0.3463 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2888 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= 0.136 Angle : 0.862 11.391 17590 Z= 0.371 Chirality : 0.060 0.392 2050 Planarity : 0.004 0.043 1474 Dihedral : 18.749 176.640 3506 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.01 % Allowed : 25.68 % Favored : 71.31 % 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: 0.23 (0.30), residues: 865 helix: 1.70 (0.28), residues: 341 sheet: -1.43 (0.52), residues: 94 loop : -0.72 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 392 TYR 0.010 0.001 TYR A 426 PHE 0.017 0.002 PHE A 801 TRP 0.013 0.001 TRP A 704 HIS 0.008 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (12248) covalent geometry : angle 0.86213 / 0.37 (17590) hydrogen bonds : bond 0.04098 / 2.64 ( 494) hydrogen bonds : angle 3.80989 / 2.76 ( 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 86 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8471 (t0) cc_final: 0.8160 (t0) REVERT: A 290 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6237 (pp) REVERT: A 704 TRP cc_start: 0.8073 (t60) cc_final: 0.7742 (t60) REVERT: A 860 LEU cc_start: 0.8483 (mm) cc_final: 0.8212 (mp) outliers start: 22 outliers final: 18 residues processed: 81 average time/residue: 0.1186 time to fit residues: 13.7406 Evaluate side-chains 74 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 100 THR 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 305 THR 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 540 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 Chi-restraints excluded: chain A residue 858 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 65 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 102 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 103 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 282 HIS ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN ** A 830 ASN ** 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 = 0.4400 r_free = 0.4400 target = 0.158627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.113788 restraints weight = 27117.430| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.70 r_work: 0.3462 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12248 Z= 0.187 Angle : 0.877 10.363 17590 Z= 0.377 Chirality : 0.059 0.355 2050 Planarity : 0.004 0.044 1474 Dihedral : 18.703 177.639 3506 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.09 % Favored : 94.80 % Rotamer: Outliers : 3.01 % Allowed : 25.68 % Favored : 71.31 % 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: 0.22 (0.30), residues: 865 helix: 1.74 (0.28), residues: 341 sheet: -1.59 (0.53), residues: 96 loop : -0.73 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 506 TYR 0.006 0.001 TYR A 61 PHE 0.021 0.002 PHE A 384 TRP 0.021 0.001 TRP A 398 HIS 0.009 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (12248) covalent geometry : angle 0.87701 / 0.38 (17590) hydrogen bonds : bond 0.04405 / 2.82 ( 494) hydrogen bonds : angle 3.84393 / 2.79 ( 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 81 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8506 (t0) cc_final: 0.8204 (t0) REVERT: A 290 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6190 (pp) REVERT: A 704 TRP cc_start: 0.8058 (t60) cc_final: 0.7731 (t60) REVERT: A 860 LEU cc_start: 0.8533 (mm) cc_final: 0.8259 (mp) outliers start: 22 outliers final: 19 residues processed: 78 average time/residue: 0.1052 time to fit residues: 12.1343 Evaluate side-chains 75 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 100 THR 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 274 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 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 820 VAL 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: 20.0000 chunk 60 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 86 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN ** 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 = 0.4394 r_free = 0.4394 target = 0.158296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.108950 restraints weight = 26883.768| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.69 r_work: 0.3481 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12248 Z= 0.178 Angle : 0.878 13.813 17590 Z= 0.377 Chirality : 0.059 0.355 2050 Planarity : 0.004 0.042 1474 Dihedral : 18.711 176.887 3506 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.97 % Favored : 94.91 % Rotamer: Outliers : 3.14 % Allowed : 25.82 % Favored : 71.04 % 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 (0.30), residues: 865 helix: 1.74 (0.28), residues: 342 sheet: -1.56 (0.53), residues: 96 loop : -0.72 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 300 TYR 0.009 0.001 TYR A 426 PHE 0.018 0.002 PHE A 384 TRP 0.012 0.001 TRP A 398 HIS 0.012 0.002 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (12248) covalent geometry : angle 0.87818 / 0.38 (17590) hydrogen bonds : bond 0.04385 / 2.81 ( 494) hydrogen bonds : angle 3.80961 / 2.76 ( 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 82 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8448 (t0) cc_final: 0.8164 (t0) REVERT: A 290 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6112 (pp) REVERT: A 704 TRP cc_start: 0.8065 (t60) cc_final: 0.7825 (t60) REVERT: A 860 LEU cc_start: 0.8559 (mm) cc_final: 0.8287 (mp) outliers start: 23 outliers final: 19 residues processed: 76 average time/residue: 0.1076 time to fit residues: 12.0171 Evaluate side-chains 75 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 107 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 274 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 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 655 ASN 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: 9.9990 chunk 102 optimal weight: 40.0000 chunk 23 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 37 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.158615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.113046 restraints weight = 27014.373| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.70 r_work: 0.3462 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12248 Z= 0.163 Angle : 0.868 10.370 17590 Z= 0.374 Chirality : 0.059 0.354 2050 Planarity : 0.004 0.041 1474 Dihedral : 18.696 176.547 3506 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.09 % Favored : 94.80 % Rotamer: Outliers : 3.01 % Allowed : 25.55 % Favored : 71.45 % 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 (0.30), residues: 865 helix: 1.78 (0.28), residues: 342 sheet: -1.53 (0.53), residues: 96 loop : -0.76 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 300 TYR 0.008 0.001 TYR A 426 PHE 0.039 0.002 PHE A 165 TRP 0.023 0.001 TRP A 398 HIS 0.008 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (12248) covalent geometry : angle 0.86756 / 0.37 (17590) hydrogen bonds : bond 0.04297 / 2.75 ( 494) hydrogen bonds : angle 3.83528 / 2.78 ( 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 80 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8494 (t0) cc_final: 0.8198 (t0) REVERT: A 290 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6132 (pp) REVERT: A 704 TRP cc_start: 0.8039 (t60) cc_final: 0.7815 (t60) REVERT: A 860 LEU cc_start: 0.8570 (mm) cc_final: 0.8299 (mp) outliers start: 22 outliers final: 20 residues processed: 76 average time/residue: 0.1080 time to fit residues: 12.0931 Evaluate side-chains 79 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 100 THR 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 274 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 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 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: 1.9990 chunk 60 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 57 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.159949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.111303 restraints weight = 27138.268| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.68 r_work: 0.3515 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3170 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= 0.138 Angle : 0.862 10.918 17590 Z= 0.370 Chirality : 0.059 0.350 2050 Planarity : 0.004 0.040 1474 Dihedral : 18.677 176.169 3506 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.62 % Favored : 95.26 % Rotamer: Outliers : 2.32 % Allowed : 26.50 % 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: 0.25 (0.30), residues: 865 helix: 1.78 (0.28), residues: 341 sheet: -1.44 (0.53), residues: 96 loop : -0.76 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 605 TYR 0.011 0.001 TYR A 426 PHE 0.049 0.002 PHE A 165 TRP 0.014 0.001 TRP A 398 HIS 0.008 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (12248) covalent geometry : angle 0.86189 / 0.37 (17590) hydrogen bonds : bond 0.04189 / 2.70 ( 494) hydrogen bonds : angle 3.79135 / 2.75 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3172.87 seconds wall clock time: 55 minutes 4.58 seconds (3304.58 seconds total)