Starting phenix.real_space_refine on Tue Aug 4 18:54:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11gj_75678/08_2026/11gj_75678.cif Found real_map, /net/cci-nas-00/data/ceres_data/11gj_75678/08_2026/11gj_75678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11gj_75678/08_2026/11gj_75678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11gj_75678/08_2026/11gj_75678.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11gj_75678/08_2026/11gj_75678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11gj_75678/08_2026/11gj_75678.map" } resolution = 3.3 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= 0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 40 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 3734 2.51 5 N 1092 2.21 5 O 1217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6116 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5283 Classifications: {'peptide': 660} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 618} Chain breaks: 5 Chain: "B" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 431 Classifications: {'RNA': 20} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 17} Chain: "C" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 401 Classifications: {'DNA': 1, 'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 17} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.63, per 1000 atoms: 0.27 Number of scatterers: 6116 At special positions: 0 Unit cell: (77.7, 81.4, 111, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 40 15.00 Mg 1 11.99 O 1217 8.00 N 1092 7.00 C 3734 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: 0.55 Conformation dependent library (CDL) restraints added in 361.2 milliseconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 5 sheets defined 36.5% alpha, 19.4% beta 16 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 68 through 82 Processing helix chain 'A' and resid 139 through 148 removed outlier: 4.072A pdb=" N LEU A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 358 through 368 removed outlier: 3.901A pdb=" N ARG A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 391 through 397 Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.578A pdb=" N MET A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 538 removed outlier: 4.378A pdb=" N ALA A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 removed outlier: 3.552A pdb=" N GLN A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 554' Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.580A pdb=" N VAL A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 583 removed outlier: 3.570A pdb=" N ARG A 583 " --> pdb=" O PRO A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 583' Processing helix chain 'A' and resid 584 through 589 removed outlier: 4.113A pdb=" N GLN A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 658 Processing helix chain 'A' and resid 675 through 693 removed outlier: 3.971A pdb=" N LEU A 685 " --> pdb=" O HIS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 787 removed outlier: 3.711A pdb=" N CYS A 787 " --> pdb=" O THR A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 817 Processing helix chain 'A' and resid 839 through 846 Processing helix chain 'A' and resid 849 through 853 Processing sheet with id=AA1, first strand: chain 'A' and resid 625 through 632 removed outlier: 5.020A pdb=" N PHE A 593 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE A 702 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A 770 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE A 704 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 734 " --> pdb=" O CYS A 751 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 406 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 177 removed outlier: 4.076A pdb=" N MET A 213 " --> pdb=" O MET A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 removed outlier: 5.716A pdb=" N GLU A 58 " --> pdb=" O TRP A 134 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N TRP A 134 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASP A 60 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ILE A 132 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 130 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 427 through 428 Processing sheet with id=AA5, first strand: chain 'A' and resid 491 through 494 removed outlier: 4.166A pdb=" N PHE A 491 " --> pdb=" O TRP A 451 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 493 " --> pdb=" O ILE A 453 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.70 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: 1069 1.32 - 1.45: 1765 1.45 - 1.57: 3374 1.57 - 1.69: 78 1.69 - 1.82: 51 Bond restraints: 6337 Sorted by residual: bond pdb=" C2 G C 11 " pdb=" N2 G C 11 " ideal model delta sigma weight residual 1.341 1.303 0.038 1.00e-02 1.00e+04 1.44e+01 bond pdb=" CA PRO A 601 " pdb=" C PRO A 601 " ideal model delta sigma weight residual 1.514 1.535 -0.021 5.50e-03 3.31e+04 1.43e+01 bond pdb=" C5' G C 11 " pdb=" C4' G C 11 " ideal model delta sigma weight residual 1.508 1.533 -0.025 7.00e-03 2.04e+04 1.29e+01 bond pdb=" CZ ARG A 179 " pdb=" NH2 ARG A 179 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.30e-02 5.92e+03 1.28e+01 bond pdb=" C GLY A 606 " pdb=" O GLY A 606 " ideal model delta sigma weight residual 1.238 1.201 0.037 1.12e-02 7.97e+03 1.07e+01 ... (remaining 6332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 8073 2.74 - 5.47: 636 5.47 - 8.21: 34 8.21 - 10.94: 17 10.94 - 13.67: 9 Bond angle restraints: 8769 Sorted by residual: angle pdb=" C3' U B 19 " pdb=" O3' U B 19 " pdb=" P U B 20 " ideal model delta sigma weight residual 119.70 106.03 13.67 1.20e+00 6.94e-01 1.30e+02 angle pdb=" C3' U B 8 " pdb=" O3' U B 8 " pdb=" P G B 9 " ideal model delta sigma weight residual 119.70 106.93 12.77 1.20e+00 6.94e-01 1.13e+02 angle pdb=" C3' G B 18 " pdb=" O3' G B 18 " pdb=" P U B 19 " ideal model delta sigma weight residual 119.70 107.10 12.60 1.20e+00 6.94e-01 1.10e+02 angle pdb=" C3' U B 17 " pdb=" O3' U B 17 " pdb=" P G B 18 " ideal model delta sigma weight residual 119.70 107.55 12.15 1.20e+00 6.94e-01 1.02e+02 angle pdb=" C3' G B 16 " pdb=" O3' G B 16 " pdb=" P U B 17 " ideal model delta sigma weight residual 119.70 108.11 11.59 1.20e+00 6.94e-01 9.33e+01 ... (remaining 8764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 3396 17.25 - 34.49: 301 34.49 - 51.74: 99 51.74 - 68.98: 58 68.98 - 86.23: 16 Dihedral angle restraints: 3870 sinusoidal: 1947 harmonic: 1923 Sorted by residual: dihedral pdb=" CD ARG A 710 " pdb=" NE ARG A 710 " pdb=" CZ ARG A 710 " pdb=" NH1 ARG A 710 " ideal model delta sinusoidal sigma weight residual 0.00 -65.37 65.37 1 1.00e+01 1.00e-02 5.60e+01 dihedral pdb=" CA ILE A 740 " pdb=" C ILE A 740 " pdb=" N THR A 741 " pdb=" CA THR A 741 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA PHE A 746 " pdb=" C PHE A 746 " pdb=" N ASP A 747 " pdb=" CA ASP A 747 " ideal model delta harmonic sigma weight residual -180.00 -160.08 -19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 3867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 849 0.112 - 0.225: 119 0.225 - 0.337: 4 0.337 - 0.449: 32 0.449 - 0.561: 3 Chirality restraints: 1007 Sorted by residual: chirality pdb=" P A C 3 " pdb=" OP1 A C 3 " pdb=" OP2 A C 3 " pdb=" O5' A C 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.88e+00 chirality pdb=" P U B 1 " pdb=" OP1 U B 1 " pdb=" OP2 U B 1 " pdb=" O5' U B 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" P A C 22 " pdb=" OP1 A C 22 " pdb=" OP2 A C 22 " pdb=" O5' A C 22 " both_signs ideal model delta sigma weight residual True 2.34 -2.80 -0.46 2.00e-01 2.50e+01 5.30e+00 ... (remaining 1004 not shown) Planarity restraints: 986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 710 " -0.998 9.50e-02 1.11e+02 4.47e-01 1.21e+02 pdb=" NE ARG A 710 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG A 710 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 710 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 710 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 12 " -0.125 2.00e-02 2.50e+03 5.47e-02 8.24e+01 pdb=" N9 A C 12 " 0.011 2.00e-02 2.50e+03 pdb=" C8 A C 12 " 0.056 2.00e-02 2.50e+03 pdb=" N7 A C 12 " 0.037 2.00e-02 2.50e+03 pdb=" C5 A C 12 " 0.020 2.00e-02 2.50e+03 pdb=" C6 A C 12 " -0.016 2.00e-02 2.50e+03 pdb=" N6 A C 12 " -0.090 2.00e-02 2.50e+03 pdb=" N1 A C 12 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A C 12 " 0.031 2.00e-02 2.50e+03 pdb=" N3 A C 12 " 0.041 2.00e-02 2.50e+03 pdb=" C4 A C 12 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 57 " -0.091 2.00e-02 2.50e+03 5.41e-02 5.86e+01 pdb=" CG TYR A 57 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 57 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR A 57 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR A 57 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR A 57 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR A 57 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 57 " -0.091 2.00e-02 2.50e+03 ... (remaining 983 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1739 2.84 - 3.36: 5309 3.36 - 3.87: 10167 3.87 - 4.39: 12035 4.39 - 4.90: 19918 Nonbonded interactions: 49168 Sorted by model distance: nonbonded pdb=" NE2 GLN A 545 " pdb=" O CYS A 546 " model vdw 2.326 3.120 nonbonded pdb=" OP1 A C 12 " pdb="MG MG A 901 " model vdw 2.377 2.170 nonbonded pdb=" OH TYR A 804 " pdb=" OP2 G B 5 " model vdw 2.382 3.040 nonbonded pdb=" O ARG A 423 " pdb=" NZ LYS A 425 " model vdw 2.442 3.120 nonbonded pdb=" NH1 ARG A 583 " pdb=" O ALA A 620 " model vdw 2.475 3.120 ... (remaining 49163 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: 0.010 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.360 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 : 0.010 0.047 6337 Z= 0.624 Angle : 1.525 13.675 8769 Z= 1.080 Chirality : 0.102 0.561 1007 Planarity : 0.018 0.447 986 Dihedral : 16.999 86.231 2622 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.35 % Allowed : 8.64 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.32), residues: 648 helix: 0.46 (0.33), residues: 232 sheet: -0.20 (0.42), residues: 159 loop : -1.40 (0.35), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 28 TYR 0.091 0.009 TYR A 57 PHE 0.063 0.007 PHE A 156 TRP 0.032 0.009 TRP A 769 HIS 0.013 0.002 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00967 / 0.62 ( 6337) covalent geometry : angle 1.52450 / 1.08 ( 8769) hydrogen bonds : bond 0.17272 / 11.40 ( 288) hydrogen bonds : angle 7.46011 / 5.23 ( 778) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.232 Fit side-chains REVERT: A 78 MET cc_start: 0.8129 (tmm) cc_final: 0.7917 (tmm) REVERT: A 104 MET cc_start: 0.8573 (mmm) cc_final: 0.8324 (tpp) REVERT: A 204 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8450 (tt0) REVERT: A 220 SER cc_start: 0.8360 (t) cc_final: 0.7825 (m) REVERT: A 637 GLU cc_start: 0.8071 (tp30) cc_final: 0.7724 (tt0) REVERT: A 654 TYR cc_start: 0.8680 (t80) cc_final: 0.8422 (t80) outliers start: 2 outliers final: 0 residues processed: 94 average time/residue: 0.1404 time to fit residues: 15.8344 Evaluate side-chains 76 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 711 HIS A 772 ASN A 807 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100927 restraints weight = 7572.839| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.07 r_work: 0.2899 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6337 Z= 0.135 Angle : 0.556 5.035 8769 Z= 0.305 Chirality : 0.043 0.154 1007 Planarity : 0.005 0.042 986 Dihedral : 16.062 73.962 1323 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.04 % Allowed : 10.54 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.33), residues: 648 helix: 1.12 (0.35), residues: 235 sheet: -0.24 (0.42), residues: 157 loop : -1.14 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 72 TYR 0.009 0.001 TYR A 749 PHE 0.016 0.001 PHE A 94 TRP 0.020 0.002 TRP A 211 HIS 0.003 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 6337) covalent geometry : angle 0.55619 / 0.31 ( 8769) hydrogen bonds : bond 0.04843 / 3.25 ( 288) hydrogen bonds : angle 5.01491 / 3.60 ( 778) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.211 Fit side-chains REVERT: A 104 MET cc_start: 0.8646 (mmm) cc_final: 0.8426 (tpp) REVERT: A 137 CYS cc_start: 0.8554 (m) cc_final: 0.8132 (t) REVERT: A 172 MET cc_start: 0.8827 (ttm) cc_final: 0.8626 (ttp) REVERT: A 220 SER cc_start: 0.8079 (t) cc_final: 0.7590 (m) REVERT: A 531 GLU cc_start: 0.8412 (tp30) cc_final: 0.8205 (tp30) REVERT: A 804 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.8040 (m-80) outliers start: 6 outliers final: 3 residues processed: 87 average time/residue: 0.0998 time to fit residues: 11.0987 Evaluate side-chains 77 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 804 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 24 optimal weight: 7.9990 chunk 27 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN ** A 441 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 = 0.3404 r_free = 0.3404 target = 0.126919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.096351 restraints weight = 7660.462| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.08 r_work: 0.2823 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6337 Z= 0.210 Angle : 0.566 5.158 8769 Z= 0.303 Chirality : 0.044 0.144 1007 Planarity : 0.005 0.038 986 Dihedral : 15.244 73.789 1320 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.73 % Allowed : 13.64 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.32), residues: 648 helix: 1.16 (0.35), residues: 229 sheet: -0.54 (0.40), residues: 161 loop : -1.29 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.015 0.002 TYR A 749 PHE 0.017 0.002 PHE A 94 TRP 0.012 0.002 TRP A 134 HIS 0.006 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 ( 6337) covalent geometry : angle 0.56644 / 0.30 ( 8769) hydrogen bonds : bond 0.05024 / 3.25 ( 288) hydrogen bonds : angle 4.69216 / 3.33 ( 778) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.242 Fit side-chains REVERT: A 73 GLU cc_start: 0.8430 (tp30) cc_final: 0.8193 (mm-30) REVERT: A 137 CYS cc_start: 0.8407 (m) cc_final: 0.8195 (t) REVERT: A 395 ARG cc_start: 0.7823 (mmt180) cc_final: 0.7620 (mmm160) REVERT: A 400 MET cc_start: 0.8237 (mtp) cc_final: 0.7870 (mtm) REVERT: A 531 GLU cc_start: 0.8444 (tp30) cc_final: 0.8204 (tp30) REVERT: A 726 LYS cc_start: 0.8386 (ttmt) cc_final: 0.7961 (ttpp) REVERT: A 804 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8127 (m-80) outliers start: 10 outliers final: 6 residues processed: 86 average time/residue: 0.0993 time to fit residues: 11.0024 Evaluate side-chains 83 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 46 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.130312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.100111 restraints weight = 7560.508| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.02 r_work: 0.2878 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6337 Z= 0.113 Angle : 0.476 5.015 8769 Z= 0.258 Chirality : 0.040 0.133 1007 Planarity : 0.004 0.039 986 Dihedral : 15.129 73.750 1320 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.38 % Allowed : 15.20 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.33), residues: 648 helix: 1.33 (0.35), residues: 230 sheet: -0.50 (0.40), residues: 163 loop : -1.25 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 668 TYR 0.010 0.001 TYR A 749 PHE 0.010 0.001 PHE A 94 TRP 0.008 0.001 TRP A 211 HIS 0.003 0.001 HIS A 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 6337) covalent geometry : angle 0.47613 / 0.26 ( 8769) hydrogen bonds : bond 0.03844 / 2.58 ( 288) hydrogen bonds : angle 4.39798 / 3.12 ( 778) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.215 Fit side-chains REVERT: A 73 GLU cc_start: 0.8456 (tp30) cc_final: 0.8190 (mm-30) REVERT: A 531 GLU cc_start: 0.8381 (tp30) cc_final: 0.8167 (tp30) REVERT: A 726 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7887 (ttpp) REVERT: A 804 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.8091 (m-80) outliers start: 8 outliers final: 3 residues processed: 83 average time/residue: 0.0851 time to fit residues: 9.3788 Evaluate side-chains 78 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.101737 restraints weight = 7648.153| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.06 r_work: 0.2888 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6337 Z= 0.116 Angle : 0.473 5.047 8769 Z= 0.253 Chirality : 0.040 0.130 1007 Planarity : 0.004 0.039 986 Dihedral : 15.012 73.747 1320 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.38 % Allowed : 15.03 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.33), residues: 648 helix: 1.41 (0.35), residues: 230 sheet: -0.42 (0.40), residues: 163 loop : -1.31 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.010 0.001 TYR A 749 PHE 0.008 0.001 PHE A 94 TRP 0.007 0.001 TRP A 211 HIS 0.002 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 6337) covalent geometry : angle 0.47337 / 0.25 ( 8769) hydrogen bonds : bond 0.03744 / 2.51 ( 288) hydrogen bonds : angle 4.27380 / 3.04 ( 778) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.219 Fit side-chains REVERT: A 400 MET cc_start: 0.8205 (mtp) cc_final: 0.7881 (mtm) REVERT: A 531 GLU cc_start: 0.8453 (tp30) cc_final: 0.8252 (tp30) REVERT: A 726 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7906 (ttpp) REVERT: A 804 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.8143 (m-80) outliers start: 8 outliers final: 5 residues processed: 79 average time/residue: 0.0919 time to fit residues: 9.6135 Evaluate side-chains 78 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.136628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.106560 restraints weight = 7405.941| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.01 r_work: 0.2888 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6337 Z= 0.124 Angle : 0.472 5.270 8769 Z= 0.252 Chirality : 0.040 0.128 1007 Planarity : 0.004 0.037 986 Dihedral : 14.985 73.756 1320 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.73 % Allowed : 16.58 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.33), residues: 648 helix: 1.31 (0.35), residues: 236 sheet: -0.49 (0.40), residues: 165 loop : -1.37 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.010 0.001 TYR A 749 PHE 0.008 0.001 PHE A 748 TRP 0.007 0.001 TRP A 211 HIS 0.002 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 6337) covalent geometry : angle 0.47157 / 0.25 ( 8769) hydrogen bonds : bond 0.03739 / 2.50 ( 288) hydrogen bonds : angle 4.23563 / 3.01 ( 778) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.222 Fit side-chains REVERT: A 726 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7916 (ttpp) REVERT: A 804 TYR cc_start: 0.8870 (OUTLIER) cc_final: 0.8155 (m-80) outliers start: 10 outliers final: 7 residues processed: 82 average time/residue: 0.0890 time to fit residues: 9.7115 Evaluate side-chains 80 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 53 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 0.1980 chunk 68 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.126714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.096295 restraints weight = 7608.883| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.06 r_work: 0.2847 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6337 Z= 0.215 Angle : 0.539 5.573 8769 Z= 0.284 Chirality : 0.043 0.131 1007 Planarity : 0.005 0.036 986 Dihedral : 14.926 73.841 1320 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.90 % Allowed : 16.41 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.32), residues: 648 helix: 1.19 (0.35), residues: 236 sheet: -0.70 (0.39), residues: 165 loop : -1.53 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 534 TYR 0.012 0.002 TYR A 749 PHE 0.012 0.002 PHE A 704 TRP 0.008 0.001 TRP A 211 HIS 0.005 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.21 ( 6337) covalent geometry : angle 0.53905 / 0.28 ( 8769) hydrogen bonds : bond 0.04701 / 3.07 ( 288) hydrogen bonds : angle 4.42071 / 3.12 ( 778) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.222 Fit side-chains REVERT: A 726 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7982 (ttpp) REVERT: A 804 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.8093 (m-80) outliers start: 11 outliers final: 8 residues processed: 77 average time/residue: 0.0905 time to fit residues: 9.2478 Evaluate side-chains 77 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.2980 chunk 61 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 51 optimal weight: 0.0970 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.132024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.100941 restraints weight = 7573.150| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.16 r_work: 0.2862 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6337 Z= 0.101 Angle : 0.458 5.036 8769 Z= 0.247 Chirality : 0.039 0.132 1007 Planarity : 0.004 0.041 986 Dihedral : 14.916 73.782 1320 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.21 % Allowed : 17.10 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.33), residues: 648 helix: 1.37 (0.35), residues: 236 sheet: -0.51 (0.40), residues: 165 loop : -1.39 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 179 TYR 0.010 0.001 TYR A 749 PHE 0.007 0.001 PHE A 748 TRP 0.009 0.001 TRP A 435 HIS 0.002 0.000 HIS A 764 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 6337) covalent geometry : angle 0.45753 / 0.25 ( 8769) hydrogen bonds : bond 0.03563 / 2.42 ( 288) hydrogen bonds : angle 4.20393 / 2.98 ( 778) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.205 Fit side-chains REVERT: A 726 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7900 (ttpp) REVERT: A 804 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.8123 (m-80) outliers start: 7 outliers final: 5 residues processed: 77 average time/residue: 0.0904 time to fit residues: 9.2037 Evaluate side-chains 76 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 0.0020 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.137734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.107543 restraints weight = 7404.339| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.03 r_work: 0.2905 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6337 Z= 0.107 Angle : 0.451 5.095 8769 Z= 0.241 Chirality : 0.039 0.129 1007 Planarity : 0.004 0.038 986 Dihedral : 14.837 73.758 1320 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.21 % Allowed : 17.62 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.33), residues: 648 helix: 1.44 (0.35), residues: 236 sheet: -0.44 (0.40), residues: 165 loop : -1.36 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 534 TYR 0.009 0.001 TYR A 749 PHE 0.009 0.001 PHE A 748 TRP 0.007 0.001 TRP A 211 HIS 0.002 0.000 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 6337) covalent geometry : angle 0.45080 / 0.24 ( 8769) hydrogen bonds : bond 0.03537 / 2.38 ( 288) hydrogen bonds : angle 4.14231 / 2.93 ( 778) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.215 Fit side-chains REVERT: A 726 LYS cc_start: 0.8280 (ttmt) cc_final: 0.7928 (ttpp) REVERT: A 804 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.8157 (m-80) outliers start: 7 outliers final: 5 residues processed: 77 average time/residue: 0.0998 time to fit residues: 9.9777 Evaluate side-chains 77 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 61 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.095731 restraints weight = 7706.073| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.08 r_work: 0.2840 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6337 Z= 0.208 Angle : 0.540 6.153 8769 Z= 0.282 Chirality : 0.043 0.132 1007 Planarity : 0.005 0.036 986 Dihedral : 14.697 73.852 1320 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.38 % Allowed : 17.62 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.32), residues: 648 helix: 1.26 (0.35), residues: 236 sheet: -0.71 (0.39), residues: 165 loop : -1.50 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 534 TYR 0.011 0.002 TYR A 749 PHE 0.012 0.002 PHE A 704 TRP 0.006 0.001 TRP A 211 HIS 0.005 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 ( 6337) covalent geometry : angle 0.53970 / 0.28 ( 8769) hydrogen bonds : bond 0.04615 / 3.01 ( 288) hydrogen bonds : angle 4.32655 / 3.05 ( 778) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.223 Fit side-chains REVERT: A 726 LYS cc_start: 0.8310 (ttmt) cc_final: 0.7947 (ttpp) REVERT: A 804 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8096 (m-80) outliers start: 8 outliers final: 6 residues processed: 76 average time/residue: 0.0983 time to fit residues: 9.7407 Evaluate side-chains 76 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 804 TYR Chi-restraints excluded: chain A residue 846 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 3 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.101330 restraints weight = 7505.895| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.03 r_work: 0.2887 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6337 Z= 0.114 Angle : 0.461 5.051 8769 Z= 0.247 Chirality : 0.039 0.129 1007 Planarity : 0.004 0.040 986 Dihedral : 14.718 73.836 1320 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.21 % Allowed : 17.44 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.33), residues: 648 helix: 1.40 (0.35), residues: 236 sheet: -0.55 (0.39), residues: 165 loop : -1.41 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 534 TYR 0.011 0.001 TYR A 749 PHE 0.008 0.001 PHE A 748 TRP 0.009 0.001 TRP A 211 HIS 0.002 0.000 HIS A 788 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 6337) covalent geometry : angle 0.46123 / 0.25 ( 8769) hydrogen bonds : bond 0.03737 / 2.52 ( 288) hydrogen bonds : angle 4.19572 / 2.96 ( 778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1778.66 seconds wall clock time: 31 minutes 20.48 seconds (1880.48 seconds total)