Starting phenix.real_space_refine on Thu Jul 2 03:17:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dp6_47097/07_2026/9dp6_47097.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dp6_47097/07_2026/9dp6_47097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dp6_47097/07_2026/9dp6_47097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dp6_47097/07_2026/9dp6_47097.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dp6_47097/07_2026/9dp6_47097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dp6_47097/07_2026/9dp6_47097.map" } resolution = 2.81 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= -0.001 sd= 0.019 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 1 5.49 5 S 31 5.16 5 C 4011 2.51 5 N 1038 2.21 5 O 1160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6241 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 633 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "A" Number of atoms: 5586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5586 Classifications: {'peptide': 737} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 703} Chain breaks: 1 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.46, per 1000 atoms: 0.23 Number of scatterers: 6241 At special positions: 0 Unit cell: (65.27, 69.55, 140.17, 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 31 16.00 P 1 15.00 O 1160 8.00 N 1038 7.00 C 4011 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: 0.65 Conformation dependent library (CDL) restraints added in 353.1 milliseconds 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1514 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 2 sheets defined 72.8% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 4 through 20 Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 40 through 55 Processing helix chain 'B' and resid 60 through 65 removed outlier: 3.852A pdb=" N ALA B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 84 removed outlier: 3.666A pdb=" N VAL B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 33 through 52 removed outlier: 4.007A pdb=" N VAL A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 71 through 84 Processing helix chain 'A' and resid 104 through 121 Processing helix chain 'A' and resid 137 through 142 removed outlier: 3.744A pdb=" N GLN A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 177 Processing helix chain 'A' and resid 190 through 226 removed outlier: 4.495A pdb=" N LYS A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 255 Processing helix chain 'A' and resid 261 through 293 Processing helix chain 'A' and resid 296 through 325 removed outlier: 5.609A pdb=" N HIS A 310 " --> pdb=" O HIS A 306 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 329 Processing helix chain 'A' and resid 331 through 365 removed outlier: 3.666A pdb=" N MET A 337 " --> pdb=" O TYR A 333 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) Proline residue: A 340 - end of helix Proline residue: A 357 - end of helix Processing helix chain 'A' and resid 378 through 391 Processing helix chain 'A' and resid 391 through 405 removed outlier: 3.531A pdb=" N ILE A 395 " --> pdb=" O TRP A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.521A pdb=" N ALA A 409 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 438 Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 460 through 477 removed outlier: 3.730A pdb=" N VAL A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 700 removed outlier: 3.514A pdb=" N THR A 700 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'A' and resid 730 through 749 removed outlier: 3.551A pdb=" N ASP A 738 " --> pdb=" O THR A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 755 removed outlier: 4.320A pdb=" N GLY A 755 " --> pdb=" O PRO A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 798 removed outlier: 4.091A pdb=" N ASP A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR A 776 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 825 removed outlier: 3.722A pdb=" N VAL A 810 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA A 815 " --> pdb=" O VAL A 811 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 864 removed outlier: 4.151A pdb=" N ILE A 843 " --> pdb=" O PRO A 839 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 844 " --> pdb=" O MET A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 867 No H-bonds generated for 'chain 'A' and resid 865 through 867' Processing helix chain 'A' and resid 870 through 879 Processing helix chain 'A' and resid 880 through 896 Processing helix chain 'A' and resid 897 through 900 Processing helix chain 'A' and resid 902 through 922 removed outlier: 3.551A pdb=" N GLY A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 936 Processing helix chain 'A' and resid 937 through 941 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 129 removed outlier: 3.526A pdb=" N HIS A 127 " --> pdb=" O TYR A 154 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN A 152 " --> pdb=" O GLN A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 480 through 484 removed outlier: 6.847A pdb=" N ILE A 723 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A 483 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR A 721 " --> pdb=" O VAL A 483 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1033 1.31 - 1.44: 1601 1.44 - 1.56: 3670 1.56 - 1.69: 1 1.69 - 1.82: 59 Bond restraints: 6364 Sorted by residual: bond pdb=" C34 PNS B 101 " pdb=" N36 PNS B 101 " ideal model delta sigma weight residual 1.337 1.451 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C39 PNS B 101 " pdb=" N41 PNS B 101 " ideal model delta sigma weight residual 1.344 1.452 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" O27 PNS B 101 " pdb=" P24 PNS B 101 " ideal model delta sigma weight residual 1.704 1.646 0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" C34 PNS B 101 " pdb=" O35 PNS B 101 " ideal model delta sigma weight residual 1.226 1.183 0.043 2.00e-02 2.50e+03 4.62e+00 bond pdb=" C39 PNS B 101 " pdb=" O40 PNS B 101 " ideal model delta sigma weight residual 1.223 1.184 0.039 2.00e-02 2.50e+03 3.72e+00 ... (remaining 6359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 8597 2.73 - 5.46: 66 5.46 - 8.19: 12 8.19 - 10.93: 1 10.93 - 13.66: 2 Bond angle restraints: 8678 Sorted by residual: angle pdb=" CB MET A 345 " pdb=" CG MET A 345 " pdb=" SD MET A 345 " ideal model delta sigma weight residual 112.70 126.08 -13.38 3.00e+00 1.11e-01 1.99e+01 angle pdb=" CA LEU A 465 " pdb=" CB LEU A 465 " pdb=" CG LEU A 465 " ideal model delta sigma weight residual 116.30 129.96 -13.66 3.50e+00 8.16e-02 1.52e+01 angle pdb=" C PHE A 464 " pdb=" N LEU A 465 " pdb=" CA LEU A 465 " ideal model delta sigma weight residual 121.14 115.43 5.71 1.75e+00 3.27e-01 1.06e+01 angle pdb=" CA LYS B 79 " pdb=" CB LYS B 79 " pdb=" CG LYS B 79 " ideal model delta sigma weight residual 114.10 120.44 -6.34 2.00e+00 2.50e-01 1.00e+01 angle pdb=" CA LYS A 953 " pdb=" CB LYS A 953 " pdb=" CG LYS A 953 " ideal model delta sigma weight residual 114.10 119.88 -5.78 2.00e+00 2.50e-01 8.36e+00 ... (remaining 8673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 3313 17.77 - 35.54: 339 35.54 - 53.31: 92 53.31 - 71.08: 27 71.08 - 88.85: 3 Dihedral angle restraints: 3774 sinusoidal: 1420 harmonic: 2354 Sorted by residual: dihedral pdb=" CA ARG A 869 " pdb=" C ARG A 869 " pdb=" N THR A 870 " pdb=" CA THR A 870 " ideal model delta harmonic sigma weight residual 180.00 163.86 16.14 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" N ARG A 292 " pdb=" CA ARG A 292 " pdb=" CB ARG A 292 " pdb=" CG ARG A 292 " ideal model delta sinusoidal sigma weight residual -60.00 -118.06 58.06 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA GLN B 5 " pdb=" CB GLN B 5 " pdb=" CG GLN B 5 " pdb=" CD GLN B 5 " ideal model delta sinusoidal sigma weight residual 60.00 116.81 -56.81 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 3771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 710 0.037 - 0.074: 248 0.074 - 0.112: 76 0.112 - 0.149: 7 0.149 - 0.186: 2 Chirality restraints: 1043 Sorted by residual: chirality pdb=" CA THR A 928 " pdb=" N THR A 928 " pdb=" C THR A 928 " pdb=" CB THR A 928 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" C32 PNS B 101 " pdb=" C29 PNS B 101 " pdb=" C34 PNS B 101 " pdb=" O33 PNS B 101 " both_signs ideal model delta sigma weight residual False 2.33 2.50 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA ASP B 38 " pdb=" N ASP B 38 " pdb=" C ASP B 38 " pdb=" CB ASP B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 1040 not shown) Planarity restraints: 1097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 68 " -0.112 9.50e-02 1.11e+02 5.07e-02 2.37e+00 pdb=" NE ARG B 68 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 68 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 68 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 68 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 776 " -0.009 2.00e-02 2.50e+03 1.02e-02 2.06e+00 pdb=" CG TYR A 776 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 776 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 776 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 776 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 776 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 776 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 776 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 101 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 102 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.015 5.00e-02 4.00e+02 ... (remaining 1094 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 231 2.71 - 3.26: 6612 3.26 - 3.81: 10946 3.81 - 4.35: 12974 4.35 - 4.90: 22593 Nonbonded interactions: 53356 Sorted by model distance: nonbonded pdb=" O PHE A 366 " pdb=" OG1 THR A 369 " model vdw 2.163 3.040 nonbonded pdb=" OG SER A 205 " pdb=" OG SER A 901 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP B 61 " pdb=" NH1 ARG A 390 " model vdw 2.266 3.120 nonbonded pdb=" OG1 THR A 329 " pdb=" OD1 ASP A 777 " model vdw 2.278 3.040 nonbonded pdb=" O LEU A 926 " pdb=" OG SER A 930 " model vdw 2.283 3.040 ... (remaining 53351 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.320 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 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 : 0.004 0.114 6364 Z= 0.196 Angle : 0.616 13.657 8678 Z= 0.295 Chirality : 0.041 0.186 1043 Planarity : 0.004 0.051 1097 Dihedral : 16.233 88.847 2260 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.60 % Allowed : 26.30 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.30), residues: 814 helix: 1.80 (0.22), residues: 547 sheet: 2.61 (0.80), residues: 43 loop : 0.60 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 68 TYR 0.025 0.001 TYR A 776 PHE 0.008 0.001 PHE A 305 TRP 0.016 0.001 TRP A 381 HIS 0.002 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 ( 6364) covalent geometry : angle 0.61554 / 0.29 ( 8678) hydrogen bonds : bond 0.12632 / 8.52 ( 449) hydrogen bonds : angle 5.40837 / 4.09 ( 1299) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.243 Fit side-chains REVERT: B 17 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8621 (tp30) REVERT: A 145 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7947 (p0) REVERT: A 161 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 256 ASN cc_start: 0.9206 (t0) cc_final: 0.8962 (m-40) REVERT: A 347 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9169 (mm) REVERT: A 482 GLN cc_start: 0.8425 (mt0) cc_final: 0.7884 (tt0) REVERT: A 737 MET cc_start: 0.9137 (mmm) cc_final: 0.8681 (mmm) REVERT: A 807 VAL cc_start: 0.9013 (t) cc_final: 0.8753 (m) outliers start: 17 outliers final: 15 residues processed: 94 average time/residue: 0.4672 time to fit residues: 46.4723 Evaluate side-chains 101 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 923 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.0970 chunk 74 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN A 442 GLN A 834 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.085354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.063874 restraints weight = 12280.459| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.58 r_work: 0.2683 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6364 Z= 0.154 Angle : 0.538 11.058 8678 Z= 0.278 Chirality : 0.041 0.177 1043 Planarity : 0.004 0.032 1097 Dihedral : 6.428 53.049 917 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.67 % Allowed : 22.48 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.29), residues: 814 helix: 1.90 (0.22), residues: 546 sheet: 2.00 (0.76), residues: 50 loop : 0.74 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 68 TYR 0.014 0.001 TYR A 255 PHE 0.012 0.001 PHE A 251 TRP 0.016 0.001 TRP A 381 HIS 0.002 0.000 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 6364) covalent geometry : angle 0.53835 / 0.28 ( 8678) hydrogen bonds : bond 0.04245 / 2.86 ( 449) hydrogen bonds : angle 4.33044 / 3.14 ( 1299) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.253 Fit side-chains REVERT: B 17 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8524 (tp30) REVERT: A 66 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.6356 (tmt) REVERT: A 94 MET cc_start: 0.8715 (mtt) cc_final: 0.8148 (mtm) REVERT: A 161 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 256 ASN cc_start: 0.9248 (t0) cc_final: 0.8971 (m-40) REVERT: A 347 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8877 (mm) REVERT: A 482 GLN cc_start: 0.8167 (mt0) cc_final: 0.7533 (tt0) REVERT: A 737 MET cc_start: 0.9099 (mmm) cc_final: 0.8664 (mmm) REVERT: A 798 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8213 (mtp85) REVERT: A 807 VAL cc_start: 0.8696 (t) cc_final: 0.8428 (m) outliers start: 24 outliers final: 7 residues processed: 101 average time/residue: 0.4765 time to fit residues: 51.0160 Evaluate side-chains 87 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 798 ARG Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 923 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 76 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.085791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.064529 restraints weight = 12238.087| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.56 r_work: 0.2680 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6364 Z= 0.137 Angle : 0.520 10.911 8678 Z= 0.267 Chirality : 0.041 0.191 1043 Planarity : 0.004 0.034 1097 Dihedral : 6.038 63.089 900 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.36 % Allowed : 22.94 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.29), residues: 814 helix: 1.92 (0.22), residues: 545 sheet: 1.80 (0.74), residues: 50 loop : 0.71 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 68 TYR 0.015 0.001 TYR A 255 PHE 0.011 0.001 PHE A 251 TRP 0.014 0.001 TRP A 381 HIS 0.002 0.000 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6364) covalent geometry : angle 0.52012 / 0.27 ( 8678) hydrogen bonds : bond 0.03882 / 2.60 ( 449) hydrogen bonds : angle 4.18923 / 3.03 ( 1299) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.246 Fit side-chains REVERT: B 17 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8443 (tp30) REVERT: B 62 GLU cc_start: 0.9161 (mp0) cc_final: 0.8826 (pm20) REVERT: B 63 ASP cc_start: 0.8730 (m-30) cc_final: 0.8117 (m-30) REVERT: A 66 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.6297 (tmt) REVERT: A 161 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 256 ASN cc_start: 0.9267 (t0) cc_final: 0.8975 (m-40) REVERT: A 482 GLN cc_start: 0.8171 (mt0) cc_final: 0.7562 (tt0) REVERT: A 696 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7675 (tp30) REVERT: A 737 MET cc_start: 0.9136 (mmm) cc_final: 0.8687 (mmm) REVERT: A 798 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8210 (mtp85) REVERT: A 807 VAL cc_start: 0.8660 (t) cc_final: 0.8398 (m) outliers start: 22 outliers final: 7 residues processed: 100 average time/residue: 0.4790 time to fit residues: 50.7191 Evaluate side-chains 87 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 798 ARG Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 923 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.086234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.065050 restraints weight = 12247.625| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.56 r_work: 0.2703 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6364 Z= 0.127 Angle : 0.520 11.475 8678 Z= 0.265 Chirality : 0.041 0.183 1043 Planarity : 0.004 0.040 1097 Dihedral : 5.202 53.680 893 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.52 % Allowed : 22.63 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.29), residues: 814 helix: 1.95 (0.22), residues: 545 sheet: 1.67 (0.73), residues: 50 loop : 0.77 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 68 TYR 0.014 0.001 TYR A 255 PHE 0.010 0.001 PHE A 251 TRP 0.014 0.001 TRP A 381 HIS 0.002 0.000 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6364) covalent geometry : angle 0.52041 / 0.26 ( 8678) hydrogen bonds : bond 0.03697 / 2.49 ( 449) hydrogen bonds : angle 4.08568 / 2.95 ( 1299) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.200 Fit side-chains REVERT: A 66 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.6657 (tmt) REVERT: A 161 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7747 (mt-10) REVERT: A 256 ASN cc_start: 0.9275 (t0) cc_final: 0.8996 (m-40) REVERT: A 449 LEU cc_start: 0.9061 (tp) cc_final: 0.8811 (tp) REVERT: A 482 GLN cc_start: 0.8189 (mt0) cc_final: 0.7588 (tt0) REVERT: A 696 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7656 (tp30) REVERT: A 737 MET cc_start: 0.9175 (mmm) cc_final: 0.8736 (mmm) REVERT: A 770 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7990 (mtm) outliers start: 23 outliers final: 12 residues processed: 98 average time/residue: 0.4667 time to fit residues: 48.4514 Evaluate side-chains 94 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 923 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 19 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 68 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 0.0060 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN A 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.087108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.065742 restraints weight = 12358.381| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.60 r_work: 0.2709 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6364 Z= 0.115 Angle : 0.520 12.444 8678 Z= 0.262 Chirality : 0.040 0.177 1043 Planarity : 0.004 0.040 1097 Dihedral : 5.159 53.698 893 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.52 % Allowed : 23.24 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.30), residues: 814 helix: 1.95 (0.22), residues: 549 sheet: 1.55 (0.73), residues: 50 loop : 0.91 (0.45), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 68 TYR 0.012 0.001 TYR A 255 PHE 0.010 0.001 PHE A 251 TRP 0.013 0.001 TRP A 381 HIS 0.001 0.000 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 6364) covalent geometry : angle 0.52012 / 0.26 ( 8678) hydrogen bonds : bond 0.03546 / 2.38 ( 449) hydrogen bonds : angle 4.03945 / 2.93 ( 1299) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.316 Fit side-chains REVERT: B 62 GLU cc_start: 0.9147 (mp0) cc_final: 0.8829 (pm20) REVERT: B 63 ASP cc_start: 0.8772 (m-30) cc_final: 0.8221 (m-30) REVERT: A 66 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.6578 (tmt) REVERT: A 145 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7778 (p0) REVERT: A 161 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 256 ASN cc_start: 0.9267 (t0) cc_final: 0.9001 (m-40) REVERT: A 449 LEU cc_start: 0.9081 (tp) cc_final: 0.8807 (tp) REVERT: A 482 GLN cc_start: 0.8226 (mt0) cc_final: 0.7691 (tt0) REVERT: A 696 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7654 (tp30) REVERT: A 737 MET cc_start: 0.9182 (mmm) cc_final: 0.8745 (mmm) REVERT: A 770 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7966 (mtm) outliers start: 23 outliers final: 11 residues processed: 96 average time/residue: 0.4956 time to fit residues: 50.2356 Evaluate side-chains 93 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 923 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 75 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.064991 restraints weight = 12311.688| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.59 r_work: 0.2696 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6364 Z= 0.136 Angle : 0.532 12.364 8678 Z= 0.269 Chirality : 0.040 0.192 1043 Planarity : 0.004 0.043 1097 Dihedral : 5.116 52.993 893 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.21 % Allowed : 22.94 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.30), residues: 814 helix: 1.94 (0.22), residues: 549 sheet: 1.44 (0.73), residues: 50 loop : 0.88 (0.45), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 68 TYR 0.014 0.001 TYR A 255 PHE 0.009 0.001 PHE A 251 TRP 0.014 0.001 TRP A 381 HIS 0.001 0.000 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6364) covalent geometry : angle 0.53160 / 0.27 ( 8678) hydrogen bonds : bond 0.03599 / 2.44 ( 449) hydrogen bonds : angle 4.01052 / 2.91 ( 1299) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.211 Fit side-chains REVERT: A 66 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.6502 (tmt) REVERT: A 145 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7749 (p0) REVERT: A 161 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7841 (mt-10) REVERT: A 256 ASN cc_start: 0.9257 (t0) cc_final: 0.9000 (m-40) REVERT: A 482 GLN cc_start: 0.8228 (mt0) cc_final: 0.7711 (tt0) REVERT: A 696 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7656 (tp30) REVERT: A 737 MET cc_start: 0.9189 (mmm) cc_final: 0.8747 (mmm) REVERT: A 770 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7958 (mtm) REVERT: A 807 VAL cc_start: 0.8551 (t) cc_final: 0.8279 (m) outliers start: 21 outliers final: 14 residues processed: 93 average time/residue: 0.4749 time to fit residues: 46.8048 Evaluate side-chains 92 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 924 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.065063 restraints weight = 12335.633| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.59 r_work: 0.2690 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6364 Z= 0.138 Angle : 0.545 13.390 8678 Z= 0.272 Chirality : 0.041 0.185 1043 Planarity : 0.004 0.048 1097 Dihedral : 5.115 52.729 893 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.21 % Allowed : 23.39 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.30), residues: 814 helix: 1.95 (0.22), residues: 549 sheet: 1.45 (0.73), residues: 50 loop : 0.90 (0.45), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 68 TYR 0.014 0.001 TYR A 255 PHE 0.009 0.001 PHE A 251 TRP 0.014 0.001 TRP A 381 HIS 0.002 0.000 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 6364) covalent geometry : angle 0.54522 / 0.27 ( 8678) hydrogen bonds : bond 0.03592 / 2.42 ( 449) hydrogen bonds : angle 4.01554 / 2.92 ( 1299) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.306 Fit side-chains REVERT: B 17 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8516 (tp30) REVERT: A 66 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.6499 (tmt) REVERT: A 145 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7745 (p0) REVERT: A 161 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7794 (mt-10) REVERT: A 256 ASN cc_start: 0.9262 (t0) cc_final: 0.9003 (m-40) REVERT: A 482 GLN cc_start: 0.8214 (mt0) cc_final: 0.7708 (tt0) REVERT: A 696 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7648 (tp30) REVERT: A 737 MET cc_start: 0.9210 (mmm) cc_final: 0.8763 (mmm) REVERT: A 770 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7975 (mtm) REVERT: A 807 VAL cc_start: 0.8550 (t) cc_final: 0.8274 (m) outliers start: 21 outliers final: 11 residues processed: 91 average time/residue: 0.5293 time to fit residues: 50.8350 Evaluate side-chains 91 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 924 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.085651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.064228 restraints weight = 12351.970| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.59 r_work: 0.2687 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6364 Z= 0.156 Angle : 0.557 13.500 8678 Z= 0.278 Chirality : 0.041 0.189 1043 Planarity : 0.004 0.051 1097 Dihedral : 5.123 51.978 893 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.75 % Allowed : 24.01 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.30), residues: 814 helix: 1.94 (0.22), residues: 547 sheet: 1.42 (0.72), residues: 50 loop : 0.79 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 68 TYR 0.015 0.001 TYR A 255 PHE 0.009 0.001 PHE A 251 TRP 0.014 0.001 TRP A 381 HIS 0.002 0.000 HIS A 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 6364) covalent geometry : angle 0.55669 / 0.28 ( 8678) hydrogen bonds : bond 0.03700 / 2.50 ( 449) hydrogen bonds : angle 4.02131 / 2.93 ( 1299) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.245 Fit side-chains REVERT: A 66 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.6459 (tmt) REVERT: A 145 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7724 (p0) REVERT: A 161 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7756 (mt-10) REVERT: A 256 ASN cc_start: 0.9262 (t0) cc_final: 0.9001 (m-40) REVERT: A 482 GLN cc_start: 0.8211 (mt0) cc_final: 0.7705 (tt0) REVERT: A 696 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7649 (tp30) REVERT: A 737 MET cc_start: 0.9184 (mmm) cc_final: 0.8743 (mmm) REVERT: A 770 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7966 (mtm) REVERT: A 807 VAL cc_start: 0.8661 (t) cc_final: 0.8400 (m) outliers start: 18 outliers final: 14 residues processed: 93 average time/residue: 0.4784 time to fit residues: 47.1104 Evaluate side-chains 92 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 924 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 69 optimal weight: 0.0000 chunk 60 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 76 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.086290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.064883 restraints weight = 12350.813| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.60 r_work: 0.2701 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6364 Z= 0.130 Angle : 0.562 14.260 8678 Z= 0.277 Chirality : 0.040 0.182 1043 Planarity : 0.004 0.058 1097 Dihedral : 5.121 52.025 893 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.60 % Allowed : 24.46 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.30), residues: 814 helix: 1.91 (0.22), residues: 550 sheet: 1.44 (0.72), residues: 50 loop : 0.89 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 68 TYR 0.014 0.001 TYR A 255 PHE 0.009 0.001 PHE A 251 TRP 0.013 0.001 TRP A 381 HIS 0.001 0.000 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 6364) covalent geometry : angle 0.56153 / 0.28 ( 8678) hydrogen bonds : bond 0.03608 / 2.44 ( 449) hydrogen bonds : angle 4.02018 / 2.93 ( 1299) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.231 Fit side-chains REVERT: B 17 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8475 (tp30) REVERT: A 66 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.6451 (tmt) REVERT: A 145 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7649 (p0) REVERT: A 161 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7718 (mt-10) REVERT: A 256 ASN cc_start: 0.9244 (t0) cc_final: 0.8984 (m-40) REVERT: A 482 GLN cc_start: 0.8185 (mt0) cc_final: 0.7683 (tt0) REVERT: A 696 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7639 (tp30) REVERT: A 737 MET cc_start: 0.9187 (mmm) cc_final: 0.8735 (mmm) REVERT: A 770 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7964 (mtm) REVERT: A 807 VAL cc_start: 0.8586 (t) cc_final: 0.8331 (m) outliers start: 17 outliers final: 10 residues processed: 96 average time/residue: 0.4691 time to fit residues: 47.7376 Evaluate side-chains 90 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 924 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 38 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.086085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.064622 restraints weight = 12278.620| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.60 r_work: 0.2683 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6364 Z= 0.143 Angle : 0.575 14.428 8678 Z= 0.283 Chirality : 0.041 0.184 1043 Planarity : 0.004 0.061 1097 Dihedral : 5.041 51.586 893 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.60 % Allowed : 24.46 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.30), residues: 814 helix: 1.87 (0.22), residues: 550 sheet: 1.45 (0.72), residues: 50 loop : 0.90 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 68 TYR 0.014 0.001 TYR A 255 PHE 0.011 0.001 PHE A 892 TRP 0.014 0.001 TRP A 381 HIS 0.001 0.000 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 6364) covalent geometry : angle 0.57523 / 0.28 ( 8678) hydrogen bonds : bond 0.03653 / 2.48 ( 449) hydrogen bonds : angle 4.00247 / 2.91 ( 1299) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1628 Ramachandran restraints generated. 814 Oldfield, 0 Emsley, 814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.234 Fit side-chains REVERT: B 17 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8443 (tp30) REVERT: A 66 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.6469 (tmt) REVERT: A 145 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7733 (p0) REVERT: A 161 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 206 MET cc_start: 0.8184 (ttm) cc_final: 0.7930 (mtp) REVERT: A 256 ASN cc_start: 0.9283 (t0) cc_final: 0.9023 (m-40) REVERT: A 482 GLN cc_start: 0.8212 (mt0) cc_final: 0.7711 (tt0) REVERT: A 696 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7636 (tp30) REVERT: A 737 MET cc_start: 0.9206 (mmm) cc_final: 0.8768 (mmm) REVERT: A 770 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7957 (mtm) outliers start: 17 outliers final: 12 residues processed: 96 average time/residue: 0.4940 time to fit residues: 50.0230 Evaluate side-chains 93 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 924 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.0970 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.086852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.065448 restraints weight = 12222.103| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.59 r_work: 0.2698 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6364 Z= 0.125 Angle : 0.576 14.565 8678 Z= 0.281 Chirality : 0.040 0.180 1043 Planarity : 0.005 0.083 1097 Dihedral : 5.018 51.647 892 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.45 % Allowed : 24.92 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.30), residues: 814 helix: 1.87 (0.22), residues: 550 sheet: 1.48 (0.73), residues: 50 loop : 0.92 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 68 TYR 0.012 0.001 TYR A 255 PHE 0.010 0.001 PHE A 892 TRP 0.012 0.001 TRP A 381 HIS 0.001 0.000 HIS A 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 6364) covalent geometry : angle 0.57590 / 0.28 ( 8678) hydrogen bonds : bond 0.03570 / 2.42 ( 449) hydrogen bonds : angle 4.01998 / 2.92 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2120.56 seconds wall clock time: 36 minutes 56.53 seconds (2216.53 seconds total)