Starting phenix.real_space_refine on Sat Aug 23 10:35:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yoj_33983/08_2025/7yoj_33983.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yoj_33983/08_2025/7yoj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yoj_33983/08_2025/7yoj_33983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yoj_33983/08_2025/7yoj_33983.map" model { file = "/net/cci-nas-00/data/ceres_data/7yoj_33983/08_2025/7yoj_33983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yoj_33983/08_2025/7yoj_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 2.47, 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: 0.69 Conformation dependent library (CDL) restraints added in 306.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.31 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: 2.70 Time building geometry restraints manager: 0.91 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=" 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=" N ASP A 219 " pdb=" CA ASP A 219 " ideal model delta sigma weight residual 1.457 1.491 -0.035 1.33e-02 5.65e+03 6.75e+00 bond pdb=" N ARG A 107 " pdb=" CA ARG A 107 " ideal model delta sigma weight residual 1.464 1.489 -0.025 9.80e-03 1.04e+04 6.64e+00 bond pdb=" N ILE A 113 " pdb=" CA ILE A 113 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.23e-02 6.61e+03 6.61e+00 bond pdb=" N VAL A 473 " pdb=" CA VAL A 473 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.17e-02 7.31e+03 6.57e+00 ... (remaining 12243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 16917 2.07 - 4.13: 580 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=" N VAL A 88 " pdb=" CA VAL A 88 " pdb=" C VAL A 88 " ideal model delta sigma weight residual 108.88 118.11 -9.23 2.16e+00 2.14e-01 1.83e+01 angle pdb=" N LEU A 331 " pdb=" CA LEU A 331 " pdb=" C LEU A 331 " ideal model delta sigma weight residual 111.36 107.06 4.30 1.09e+00 8.42e-01 1.55e+01 angle pdb=" N LEU A 38 " pdb=" CA LEU A 38 " pdb=" C LEU A 38 " ideal model delta sigma weight residual 111.71 107.19 4.52 1.15e+00 7.56e-01 1.55e+01 ... (remaining 17585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.61: 6655 34.61 - 69.23: 775 69.23 - 103.84: 93 103.84 - 138.45: 4 138.45 - 173.07: 4 Dihedral angle restraints: 7531 sinusoidal: 5022 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 7528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1865 0.085 - 0.169: 156 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.820 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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= 0.257 Angle : 0.870 10.333 17590 Z= 0.477 Chirality : 0.053 0.423 2050 Planarity : 0.007 0.135 1474 Dihedral : 24.105 173.068 5909 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 aren 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 covalent geometry : bond 0.00457 (12248) covalent geometry : angle 0.87013 (17590) hydrogen bonds : bond 0.15085 ( 494) hydrogen bonds : angle 7.14203 ( 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 : 0.227 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: 0.1126 time to fit residues: 12.5063 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 : 0.232 ------------------------------------------------------------------------------- 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: 4.9990 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... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.159350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.110523 restraints weight = 26939.746| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.69 r_work: 0.3531 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1488 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= 0.162 Angle : 0.630 7.244 17590 Z= 0.319 Chirality : 0.036 0.283 2050 Planarity : 0.005 0.085 1474 Dihedral : 24.145 168.185 4164 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.05 % Favored : 95.84 % Rotamer: Outliers : 2.19 % Allowed : 25.27 % 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 aren not related in a simple way. whole: -0.77 (0.28), residues: 865 helix: 0.67 (0.28), residues: 341 sheet: -1.76 (0.50), residues: 94 loop : -1.15 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 271 TYR 0.013 0.001 TYR A 61 PHE 0.019 0.002 PHE A 384 TRP 0.012 0.001 TRP A 244 HIS 0.009 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00340 (12248) covalent geometry : angle 0.62976 (17590) hydrogen bonds : bond 0.04585 ( 494) hydrogen bonds : angle 4.26052 ( 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 77 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8212 (t0) cc_final: 0.7923 (t0) outliers start: 16 outliers final: 14 residues processed: 73 average time/residue: 0.1203 time to fit residues: 12.1984 Evaluate side-chains 67 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 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 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 305 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 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: 1.9990 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 66 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4425 r_free = 0.4425 target = 0.159877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.111138 restraints weight = 27076.126| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.74 r_work: 0.3538 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12248 Z= 0.139 Angle : 0.606 11.586 17590 Z= 0.305 Chirality : 0.035 0.239 2050 Planarity : 0.005 0.068 1474 Dihedral : 24.038 169.340 4156 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.62 % Favored : 95.26 % Rotamer: Outliers : 2.60 % Allowed : 24.73 % 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 aren not related in a simple way. whole: -0.22 (0.29), residues: 865 helix: 1.35 (0.28), residues: 340 sheet: -1.70 (0.51), residues: 94 loop : -0.99 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.015 0.001 TYR A 61 PHE 0.017 0.001 PHE A 384 TRP 0.017 0.001 TRP A 704 HIS 0.009 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00291 (12248) covalent geometry : angle 0.60637 (17590) hydrogen bonds : bond 0.03971 ( 494) hydrogen bonds : angle 3.88851 ( 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 86 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8347 (t0) cc_final: 0.8032 (t0) REVERT: A 290 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6092 (pp) REVERT: A 351 MET cc_start: 0.7675 (mtm) cc_final: 0.7404 (mtp) outliers start: 19 outliers final: 14 residues processed: 81 average time/residue: 0.1101 time to fit residues: 12.2786 Evaluate side-chains 73 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 276 SER 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 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: 5.9990 chunk 26 optimal weight: 9.9990 chunk 76 optimal weight: 0.0670 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4395 r_free = 0.4395 target = 0.157353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.108037 restraints weight = 27116.239| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.70 r_work: 0.3487 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12248 Z= 0.197 Angle : 0.632 9.784 17590 Z= 0.321 Chirality : 0.037 0.248 2050 Planarity : 0.005 0.060 1474 Dihedral : 24.069 170.344 4156 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.62 % Favored : 95.26 % Rotamer: Outliers : 4.37 % Allowed : 23.77 % 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 aren not related in a simple way. whole: -0.15 (0.29), residues: 865 helix: 1.41 (0.28), residues: 341 sheet: -1.79 (0.50), residues: 96 loop : -0.92 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 107 TYR 0.012 0.001 TYR A 61 PHE 0.024 0.002 PHE A 384 TRP 0.027 0.002 TRP A 704 HIS 0.009 0.002 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00421 (12248) covalent geometry : angle 0.63200 (17590) hydrogen bonds : bond 0.04363 ( 494) hydrogen bonds : angle 3.91744 ( 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 89 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 57 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8397 (t0) cc_final: 0.8110 (t0) REVERT: A 290 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6129 (pp) REVERT: A 334 MET cc_start: 0.7641 (ptt) cc_final: 0.7390 (ptt) outliers start: 32 outliers final: 22 residues processed: 82 average time/residue: 0.1120 time to fit residues: 13.0258 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 : 0.216 ------------------------------------------------------------------------------- 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 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 378 TRP 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 706 LYS 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: 2.9990 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 102 optimal weight: 40.0000 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4409 r_free = 0.4409 target = 0.158812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.109794 restraints weight = 26985.143| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.70 r_work: 0.3521 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2407 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= 0.151 Angle : 0.598 8.380 17590 Z= 0.302 Chirality : 0.035 0.229 2050 Planarity : 0.004 0.052 1474 Dihedral : 24.041 167.875 4154 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.51 % Favored : 95.38 % Rotamer: Outliers : 4.10 % Allowed : 24.04 % 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 aren not related in a simple way. whole: 0.04 (0.29), residues: 865 helix: 1.57 (0.28), residues: 341 sheet: -1.66 (0.52), residues: 96 loop : -0.82 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 107 TYR 0.012 0.001 TYR A 426 PHE 0.016 0.002 PHE A 384 TRP 0.013 0.001 TRP A 704 HIS 0.007 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00319 (12248) covalent geometry : angle 0.59775 (17590) hydrogen bonds : bond 0.04017 ( 494) hydrogen bonds : angle 3.86045 ( 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 87 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8368 (t0) cc_final: 0.8073 (t0) REVERT: A 290 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6163 (pp) REVERT: A 373 GLU cc_start: 0.7431 (mp0) cc_final: 0.7132 (mp0) REVERT: A 860 LEU cc_start: 0.8541 (mm) cc_final: 0.8316 (mp) outliers start: 30 outliers final: 20 residues processed: 84 average time/residue: 0.1086 time to fit residues: 12.7653 Evaluate side-chains 72 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 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 378 TRP 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 698 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: 2.9990 chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 0.0980 chunk 67 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.158548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.109451 restraints weight = 26808.934| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.70 r_work: 0.3485 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2589 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= 0.138 Angle : 0.602 10.552 17590 Z= 0.302 Chirality : 0.035 0.235 2050 Planarity : 0.004 0.046 1474 Dihedral : 23.987 168.747 4154 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.62 % Favored : 95.26 % Rotamer: Outliers : 3.96 % Allowed : 25.00 % 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 aren not related in a simple way. whole: 0.11 (0.30), residues: 865 helix: 1.65 (0.28), residues: 340 sheet: -1.63 (0.52), residues: 96 loop : -0.78 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 392 TYR 0.011 0.001 TYR A 311 PHE 0.015 0.002 PHE A 801 TRP 0.020 0.001 TRP A 704 HIS 0.008 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00292 (12248) covalent geometry : angle 0.60208 (17590) hydrogen bonds : bond 0.03856 ( 494) hydrogen bonds : angle 3.82142 ( 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 89 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8435 (t0) cc_final: 0.8128 (t0) REVERT: A 290 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6145 (pp) REVERT: A 704 TRP cc_start: 0.7798 (t60) cc_final: 0.7521 (t60) outliers start: 29 outliers final: 21 residues processed: 85 average time/residue: 0.1209 time to fit residues: 14.6454 Evaluate side-chains 77 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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 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 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: 0.8980 chunk 60 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS 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 = 0.4397 r_free = 0.4397 target = 0.158527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.109454 restraints weight = 26750.448| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.69 r_work: 0.3485 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12248 Z= 0.143 Angle : 0.606 8.733 17590 Z= 0.304 Chirality : 0.035 0.228 2050 Planarity : 0.004 0.034 1474 Dihedral : 23.981 168.539 4154 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.74 % Favored : 95.14 % Rotamer: Outliers : 3.55 % Allowed : 25.00 % 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 aren not related in a simple way. whole: 0.15 (0.30), residues: 865 helix: 1.68 (0.28), residues: 340 sheet: -1.62 (0.52), residues: 96 loop : -0.76 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 392 TYR 0.014 0.001 TYR A 61 PHE 0.041 0.002 PHE A 165 TRP 0.012 0.001 TRP A 704 HIS 0.008 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00301 (12248) covalent geometry : angle 0.60566 (17590) hydrogen bonds : bond 0.03880 ( 494) hydrogen bonds : angle 3.79112 ( 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 83 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8442 (t0) cc_final: 0.8139 (t0) REVERT: A 290 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6145 (pp) REVERT: A 704 TRP cc_start: 0.7811 (t60) cc_final: 0.7520 (t60) REVERT: A 860 LEU cc_start: 0.8579 (mm) cc_final: 0.8345 (mp) outliers start: 26 outliers final: 22 residues processed: 79 average time/residue: 0.1328 time to fit residues: 14.7612 Evaluate side-chains 79 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 246 GLN 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 387 THR Chi-restraints excluded: chain A residue 425 VAL 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 698 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: 8.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 102 optimal weight: 40.0000 chunk 49 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 103 optimal weight: 40.0000 chunk 13 optimal weight: 7.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 246 GLN ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 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 = 0.4356 r_free = 0.4356 target = 0.155355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.110592 restraints weight = 26783.894| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.46 r_work: 0.3434 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12248 Z= 0.236 Angle : 0.670 9.914 17590 Z= 0.339 Chirality : 0.038 0.286 2050 Planarity : 0.005 0.039 1474 Dihedral : 24.071 169.982 4154 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.43 % Favored : 94.45 % Rotamer: Outliers : 4.23 % Allowed : 24.32 % 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 aren not related in a simple way. whole: 0.04 (0.30), residues: 865 helix: 1.59 (0.28), residues: 340 sheet: -1.71 (0.53), residues: 96 loop : -0.81 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 506 TYR 0.018 0.002 TYR A 311 PHE 0.032 0.002 PHE A 165 TRP 0.020 0.002 TRP A 244 HIS 0.008 0.002 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00506 (12248) covalent geometry : angle 0.66992 (17590) hydrogen bonds : bond 0.04523 ( 494) hydrogen bonds : angle 3.92447 ( 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 89 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 58 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8479 (t0) cc_final: 0.8165 (t0) REVERT: A 290 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6180 (pp) REVERT: A 373 GLU cc_start: 0.7632 (mp0) cc_final: 0.7264 (mp0) REVERT: A 704 TRP cc_start: 0.7960 (t60) cc_final: 0.7646 (t60) outliers start: 31 outliers final: 23 residues processed: 85 average time/residue: 0.1268 time to fit residues: 15.2094 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 : 0.331 ------------------------------------------------------------------------------- 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 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 356 LEU Chi-restraints excluded: chain A residue 378 TRP Chi-restraints excluded: chain A residue 387 THR 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 698 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 103 optimal weight: 40.0000 chunk 42 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 20 optimal weight: 0.0970 chunk 84 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS 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 = 0.4424 r_free = 0.4424 target = 0.161057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.112774 restraints weight = 26612.719| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.69 r_work: 0.3538 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12248 Z= 0.117 Angle : 0.595 7.945 17590 Z= 0.297 Chirality : 0.035 0.215 2050 Planarity : 0.004 0.039 1474 Dihedral : 23.875 168.857 4154 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.32 % Allowed : 26.09 % 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 aren not related in a simple way. whole: 0.35 (0.30), residues: 865 helix: 1.94 (0.28), residues: 340 sheet: -1.41 (0.55), residues: 96 loop : -0.78 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 392 TYR 0.014 0.001 TYR A 61 PHE 0.025 0.002 PHE A 165 TRP 0.018 0.001 TRP A 244 HIS 0.008 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00241 (12248) covalent geometry : angle 0.59529 (17590) hydrogen bonds : bond 0.03715 ( 494) hydrogen bonds : angle 3.67057 ( 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: 17 poor density : 65 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8326 (t0) cc_final: 0.8047 (t0) REVERT: A 290 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6004 (pp) REVERT: A 373 GLU cc_start: 0.7589 (mp0) cc_final: 0.7201 (mp0) outliers start: 17 outliers final: 14 residues processed: 79 average time/residue: 0.1198 time to fit residues: 13.5417 Evaluate side-chains 72 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 102 optimal weight: 40.0000 chunk 23 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 437 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 = 0.4382 r_free = 0.4382 target = 0.157675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.108371 restraints weight = 26632.834| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.70 r_work: 0.3468 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12248 Z= 0.175 Angle : 0.629 8.024 17590 Z= 0.315 Chirality : 0.037 0.253 2050 Planarity : 0.004 0.037 1474 Dihedral : 23.926 169.197 4154 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.43 % Favored : 94.45 % Rotamer: Outliers : 2.19 % Allowed : 26.37 % 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 aren not related in a simple way. whole: 0.28 (0.30), residues: 865 helix: 1.83 (0.28), residues: 341 sheet: -1.52 (0.54), residues: 96 loop : -0.75 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 107 TYR 0.015 0.001 TYR A 61 PHE 0.031 0.002 PHE A 165 TRP 0.015 0.001 TRP A 140 HIS 0.010 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00374 (12248) covalent geometry : angle 0.62881 (17590) hydrogen bonds : bond 0.04060 ( 494) hydrogen bonds : angle 3.80579 ( 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 72 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8414 (t0) cc_final: 0.8114 (t0) REVERT: A 290 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6027 (pp) REVERT: A 373 GLU cc_start: 0.7691 (mp0) cc_final: 0.7319 (mp0) REVERT: A 704 TRP cc_start: 0.7954 (t60) cc_final: 0.7683 (t60) outliers start: 16 outliers final: 15 residues processed: 71 average time/residue: 0.1336 time to fit residues: 13.1579 Evaluate side-chains 72 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS 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 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 489 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 698 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: 0.3980 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 37 optimal weight: 0.0670 chunk 57 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 33 optimal weight: 0.0670 chunk 75 optimal weight: 30.0000 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS 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 = 0.4426 r_free = 0.4426 target = 0.161570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.113289 restraints weight = 26912.194| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.70 r_work: 0.3553 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12248 Z= 0.116 Angle : 0.592 7.586 17590 Z= 0.295 Chirality : 0.034 0.206 2050 Planarity : 0.004 0.038 1474 Dihedral : 23.750 168.340 4154 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.32 % Allowed : 26.37 % 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 aren not related in a simple way. whole: 0.42 (0.30), residues: 865 helix: 1.93 (0.28), residues: 345 sheet: -1.26 (0.56), residues: 94 loop : -0.73 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 598 TYR 0.012 0.001 TYR A 61 PHE 0.018 0.001 PHE A 165 TRP 0.013 0.001 TRP A 244 HIS 0.009 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00243 (12248) covalent geometry : angle 0.59246 (17590) hydrogen bonds : bond 0.03648 ( 494) hydrogen bonds : angle 3.61955 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3081.00 seconds wall clock time: 53 minutes 29.41 seconds (3209.41 seconds total)