Starting phenix.real_space_refine on Tue Jun 10 08:50:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yoj_33983/06_2025/7yoj_33983.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yoj_33983/06_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_33983/06_2025/7yoj_33983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yoj_33983/06_2025/7yoj_33983.map" model { file = "/net/cci-nas-00/data/ceres_data/7yoj_33983/06_2025/7yoj_33983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yoj_33983/06_2025/7yoj_33983.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.69, per 1000 atoms: 0.67 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: 2.99 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 4.76 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: 6.21 Time building geometry restraints manager: 3.60 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: 1.250 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 35.350 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.580 ------------------------------------------------------------------------------- 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 : 7.98 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.002 TRP A 244 HIS 0.018 0.002 HIS A 55 PHE 0.026 0.002 PHE A 384 TYR 0.024 0.002 TYR A 21 ARG 0.010 0.001 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.15085 ( 494) hydrogen bonds : angle 7.14203 ( 1251) covalent geometry : bond 0.00457 (12248) covalent geometry : angle 0.87013 (17590) *********************** 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 : 0.948 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: 0.2912 time to fit residues: 32.4605 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 : 0.762 ------------------------------------------------------------------------------- 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 90 optimal weight: 30.0000 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 670 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.155925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.106852 restraints weight = 26632.441| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.71 r_work: 0.3460 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12248 Z= 0.250 Angle : 0.702 7.233 17590 Z= 0.358 Chirality : 0.039 0.336 2050 Planarity : 0.006 0.086 1474 Dihedral : 24.314 168.961 4164 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.20 % Favored : 94.68 % Rotamer: Outliers : 3.42 % Allowed : 23.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.28), residues: 865 helix: 0.53 (0.28), residues: 342 sheet: -2.02 (0.49), residues: 96 loop : -1.17 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 244 HIS 0.008 0.001 HIS A 55 PHE 0.029 0.002 PHE A 384 TYR 0.016 0.002 TYR A 426 ARG 0.006 0.001 ARG A 605 Details of bonding type rmsd hydrogen bonds : bond 0.05306 ( 494) hydrogen bonds : angle 4.36967 ( 1251) covalent geometry : bond 0.00535 (12248) covalent geometry : angle 0.70223 (17590) *********************** 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 87 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8392 (t0) cc_final: 0.8052 (t0) outliers start: 25 outliers final: 20 residues processed: 81 average time/residue: 0.2945 time to fit residues: 33.1559 Evaluate side-chains 74 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 81 ARG 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 276 SER Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 548 VAL 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 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 97 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 8 optimal weight: 30.0000 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4378 r_free = 0.4378 target = 0.156166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.110584 restraints weight = 27293.876| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.72 r_work: 0.3443 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2205 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= 0.225 Angle : 0.674 11.856 17590 Z= 0.341 Chirality : 0.038 0.285 2050 Planarity : 0.005 0.068 1474 Dihedral : 24.308 173.952 4156 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.55 % Favored : 94.34 % Rotamer: Outliers : 3.69 % Allowed : 25.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.29), residues: 865 helix: 1.00 (0.28), residues: 342 sheet: -2.05 (0.49), residues: 96 loop : -1.05 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 704 HIS 0.009 0.001 HIS A 55 PHE 0.025 0.002 PHE A 384 TYR 0.012 0.001 TYR A 426 ARG 0.004 0.000 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 494) hydrogen bonds : angle 4.14966 ( 1251) covalent geometry : bond 0.00485 (12248) covalent geometry : angle 0.67417 (17590) *********************** 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 87 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8446 (t0) cc_final: 0.8113 (t0) REVERT: A 290 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6031 (pp) outliers start: 27 outliers final: 20 residues processed: 82 average time/residue: 0.2587 time to fit residues: 30.2346 Evaluate side-chains 73 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 378 TRP Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 548 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 4 optimal weight: 1.9990 chunk 103 optimal weight: 40.0000 chunk 89 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 94 optimal weight: 30.0000 chunk 46 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4401 r_free = 0.4401 target = 0.158172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.108969 restraints weight = 27225.806| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.75 r_work: 0.3500 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 12248 Z= 0.157 Angle : 0.618 10.793 17590 Z= 0.311 Chirality : 0.036 0.256 2050 Planarity : 0.005 0.059 1474 Dihedral : 24.210 179.932 4154 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.86 % Favored : 95.03 % Rotamer: Outliers : 3.55 % Allowed : 25.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.29), residues: 865 helix: 1.26 (0.28), residues: 342 sheet: -2.02 (0.49), residues: 96 loop : -0.91 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.007 0.001 HIS A 55 PHE 0.017 0.002 PHE A 801 TYR 0.011 0.001 TYR A 426 ARG 0.003 0.000 ARG A 656 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 494) hydrogen bonds : angle 4.00361 ( 1251) covalent geometry : bond 0.00336 (12248) covalent geometry : angle 0.61806 (17590) *********************** 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: 26 poor density : 63 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8399 (t0) cc_final: 0.8064 (t0) REVERT: A 290 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6231 (pp) REVERT: A 334 MET cc_start: 0.7729 (ptt) cc_final: 0.7501 (ptt) REVERT: A 860 LEU cc_start: 0.8602 (mm) cc_final: 0.8339 (mp) outliers start: 26 outliers final: 17 residues processed: 86 average time/residue: 0.2925 time to fit residues: 34.7632 Evaluate side-chains 74 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 540 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 66 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 82 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 8 optimal weight: 30.0000 chunk 20 optimal weight: 0.4980 chunk 7 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.4399 r_free = 0.4399 target = 0.158086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.112763 restraints weight = 26848.075| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.46 r_work: 0.3497 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12248 Z= 0.153 Angle : 0.616 8.910 17590 Z= 0.311 Chirality : 0.036 0.248 2050 Planarity : 0.004 0.051 1474 Dihedral : 24.175 176.092 4154 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.97 % Favored : 94.91 % Rotamer: Outliers : 4.51 % Allowed : 24.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.30), residues: 865 helix: 1.43 (0.28), residues: 342 sheet: -1.86 (0.50), residues: 96 loop : -0.83 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 704 HIS 0.008 0.001 HIS A 55 PHE 0.017 0.001 PHE A 801 TYR 0.013 0.001 TYR A 61 ARG 0.004 0.000 ARG A 605 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 494) hydrogen bonds : angle 3.91615 ( 1251) covalent geometry : bond 0.00326 (12248) covalent geometry : angle 0.61605 (17590) *********************** 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 91 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 58 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8491 (t0) cc_final: 0.8160 (t0) REVERT: A 290 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6102 (pp) REVERT: A 373 GLU cc_start: 0.7458 (mp0) cc_final: 0.7221 (mp0) REVERT: A 860 LEU cc_start: 0.8582 (mm) cc_final: 0.8319 (mp) outliers start: 33 outliers final: 22 residues processed: 87 average time/residue: 0.2527 time to fit residues: 32.2280 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 : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 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 698 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 829 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 74 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 94 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 102 optimal weight: 40.0000 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.157432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.109050 restraints weight = 26877.914| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.68 r_work: 0.3503 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12248 Z= 0.159 Angle : 0.614 10.340 17590 Z= 0.311 Chirality : 0.036 0.297 2050 Planarity : 0.004 0.047 1474 Dihedral : 24.159 174.720 4154 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.97 % Favored : 94.91 % Rotamer: Outliers : 4.51 % Allowed : 24.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.30), residues: 865 helix: 1.55 (0.28), residues: 340 sheet: -1.82 (0.51), residues: 96 loop : -0.82 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.008 0.001 HIS A 55 PHE 0.019 0.002 PHE A 165 TYR 0.015 0.001 TYR A 61 ARG 0.003 0.000 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 494) hydrogen bonds : angle 3.88982 ( 1251) covalent geometry : bond 0.00336 (12248) covalent geometry : angle 0.61429 (17590) *********************** 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 94 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 61 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8432 (t0) cc_final: 0.8116 (t0) REVERT: A 290 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6088 (pp) REVERT: A 860 LEU cc_start: 0.8581 (mm) cc_final: 0.8319 (mp) outliers start: 33 outliers final: 24 residues processed: 91 average time/residue: 0.2382 time to fit residues: 31.5767 Evaluate side-chains 80 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 250 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 64 optimal weight: 0.0270 chunk 65 optimal weight: 0.0570 chunk 66 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 chunk 23 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.4114 ------------------------------------------------------------------------------- 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 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 = 0.4429 r_free = 0.4429 target = 0.161465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.113355 restraints weight = 26884.331| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.72 r_work: 0.3555 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12248 Z= 0.114 Angle : 0.591 8.182 17590 Z= 0.295 Chirality : 0.034 0.210 2050 Planarity : 0.004 0.043 1474 Dihedral : 23.934 169.371 4154 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.87 % Allowed : 26.37 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.30), residues: 865 helix: 1.95 (0.28), residues: 339 sheet: -1.42 (0.54), residues: 94 loop : -0.81 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 244 HIS 0.009 0.001 HIS A 55 PHE 0.015 0.001 PHE A 801 TYR 0.013 0.001 TYR A 61 ARG 0.003 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 494) hydrogen bonds : angle 3.65930 ( 1251) covalent geometry : bond 0.00235 (12248) covalent geometry : angle 0.59060 (17590) *********************** 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 96 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8404 (t0) cc_final: 0.8130 (t0) REVERT: A 290 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6012 (pp) REVERT: A 304 HIS cc_start: 0.6650 (t-170) cc_final: 0.6408 (t-170) REVERT: A 494 ASP cc_start: 0.8227 (t0) cc_final: 0.7074 (p0) REVERT: A 860 LEU cc_start: 0.8517 (mm) cc_final: 0.8288 (mp) outliers start: 21 outliers final: 14 residues processed: 93 average time/residue: 0.2645 time to fit residues: 35.1104 Evaluate side-chains 75 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 204 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 290 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 102 optimal weight: 40.0000 chunk 82 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 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 = 0.4361 r_free = 0.4361 target = 0.156070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.109183 restraints weight = 26519.881| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.71 r_work: 0.3426 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12248 Z= 0.204 Angle : 0.650 7.695 17590 Z= 0.328 Chirality : 0.037 0.238 2050 Planarity : 0.004 0.038 1474 Dihedral : 24.099 170.077 4154 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.43 % Favored : 94.45 % Rotamer: Outliers : 3.14 % Allowed : 26.50 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.30), residues: 865 helix: 1.75 (0.28), residues: 340 sheet: -1.74 (0.52), residues: 96 loop : -0.83 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 398 HIS 0.010 0.001 HIS A 55 PHE 0.021 0.002 PHE A 384 TYR 0.016 0.001 TYR A 61 ARG 0.004 0.000 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.04289 ( 494) hydrogen bonds : angle 3.91422 ( 1251) covalent geometry : bond 0.00439 (12248) covalent geometry : angle 0.64989 (17590) *********************** 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: 23 poor density : 58 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8510 (t0) cc_final: 0.8198 (t0) REVERT: A 290 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6089 (pp) REVERT: A 794 ASP cc_start: 0.8281 (m-30) cc_final: 0.7996 (m-30) REVERT: A 860 LEU cc_start: 0.8737 (mm) cc_final: 0.8412 (mp) outliers start: 23 outliers final: 18 residues processed: 79 average time/residue: 0.2613 time to fit residues: 29.3306 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 : 0.917 ------------------------------------------------------------------------------- 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 204 VAL Chi-restraints excluded: chain A residue 250 VAL 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 397 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 698 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 91 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 75 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 30.0000 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.155151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.105414 restraints weight = 26856.988| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.68 r_work: 0.3422 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12248 Z= 0.236 Angle : 0.678 10.764 17590 Z= 0.342 Chirality : 0.039 0.338 2050 Planarity : 0.005 0.036 1474 Dihedral : 24.171 171.236 4154 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.66 % Favored : 94.22 % Rotamer: Outliers : 3.28 % Allowed : 26.91 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.29), residues: 865 helix: 1.53 (0.28), residues: 340 sheet: -1.73 (0.53), residues: 96 loop : -0.87 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 398 HIS 0.009 0.001 HIS A 55 PHE 0.024 0.002 PHE A 384 TYR 0.015 0.001 TYR A 61 ARG 0.014 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.04443 ( 494) hydrogen bonds : angle 3.98285 ( 1251) covalent geometry : bond 0.00510 (12248) covalent geometry : angle 0.67802 (17590) *********************** 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 75 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6175 (pp) REVERT: A 860 LEU cc_start: 0.8687 (mm) cc_final: 0.8407 (mp) outliers start: 24 outliers final: 20 residues processed: 73 average time/residue: 0.2992 time to fit residues: 32.5275 Evaluate side-chains 71 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 204 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 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 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 75 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.157234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.108017 restraints weight = 26412.615| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.64 r_work: 0.3469 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12248 Z= 0.158 Angle : 0.626 8.481 17590 Z= 0.315 Chirality : 0.036 0.233 2050 Planarity : 0.004 0.038 1474 Dihedral : 24.122 170.303 4154 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.55 % Favored : 94.34 % Rotamer: Outliers : 2.87 % Allowed : 27.32 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.30), residues: 865 helix: 1.68 (0.28), residues: 340 sheet: -1.68 (0.53), residues: 96 loop : -0.83 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.009 0.001 HIS A 55 PHE 0.017 0.002 PHE A 384 TYR 0.015 0.001 TYR A 61 ARG 0.005 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 494) hydrogen bonds : angle 3.87688 ( 1251) covalent geometry : bond 0.00338 (12248) covalent geometry : angle 0.62624 (17590) ********************** 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 76 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6078 (pp) REVERT: A 860 LEU cc_start: 0.8736 (mm) cc_final: 0.8415 (mp) outliers start: 21 outliers final: 16 residues processed: 74 average time/residue: 0.2943 time to fit residues: 31.4381 Evaluate side-chains 68 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 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 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 42 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 30.0000 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4384 r_free = 0.4384 target = 0.157977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.113460 restraints weight = 26893.937| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.76 r_work: 0.3459 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3363 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= 0.141 Angle : 0.613 7.829 17590 Z= 0.308 Chirality : 0.036 0.225 2050 Planarity : 0.004 0.035 1474 Dihedral : 24.078 169.428 4154 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.97 % Favored : 94.91 % Rotamer: Outliers : 2.87 % Allowed : 27.60 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.30), residues: 865 helix: 1.74 (0.28), residues: 339 sheet: -1.59 (0.54), residues: 96 loop : -0.80 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.010 0.001 HIS A 55 PHE 0.016 0.002 PHE A 801 TYR 0.013 0.001 TYR A 61 ARG 0.006 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 494) hydrogen bonds : angle 3.83901 ( 1251) covalent geometry : bond 0.00299 (12248) covalent geometry : angle 0.61279 (17590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8106.32 seconds wall clock time: 142 minutes 38.02 seconds (8558.02 seconds total)