Starting phenix.real_space_refine on Wed Aug 5 12:44:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21dz_67605/08_2026/21dz_67605.cif Found real_map, /net/cci-nas-00/data/ceres_data/21dz_67605/08_2026/21dz_67605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21dz_67605/08_2026/21dz_67605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21dz_67605/08_2026/21dz_67605.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21dz_67605/08_2026/21dz_67605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21dz_67605/08_2026/21dz_67605.map" } resolution = 2.41 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= 0.055 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 144 5.49 5 S 20 5.16 5 C 5629 2.51 5 N 1765 2.21 5 O 2189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 9747 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 6721 Classifications: {'peptide': 842} Link IDs: {'PTRANS': 33, 'TRANS': 808} Chain breaks: 8 Chain: "B" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2053 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 5, 'rna3p_pur': 45, 'rna3p_pyr': 46} Link IDs: {'rna2p': 6, 'rna3p': 90} Chain breaks: 3 Chain: "C" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 727 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "D" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 1.74, per 1000 atoms: 0.18 Number of scatterers: 9747 At special positions: 0 Unit cell: (84, 109.2, 120.12, 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 20 16.00 P 144 15.00 O 2189 8.00 N 1765 7.00 C 5629 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: 0.67 Conformation dependent library (CDL) restraints added in 233.6 milliseconds 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 41.0% alpha, 14.5% beta 62 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 54 through 84 Processing helix chain 'A' and resid 88 through 96 removed outlier: 3.926A pdb=" N TYR A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 118 through 132 removed outlier: 3.809A pdb=" N ARG A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 166 removed outlier: 3.819A pdb=" N MET A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 177 Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'A' and resid 235 through 248 Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.687A pdb=" N VAL A 281 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 329 through 343 Processing helix chain 'A' and resid 348 through 353 removed outlier: 3.724A pdb=" N LYS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 398 Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 406 through 420 Processing helix chain 'A' and resid 422 through 434 Processing helix chain 'A' and resid 436 through 444 Processing helix chain 'A' and resid 455 through 468 Proline residue: A 464 - end of helix removed outlier: 3.570A pdb=" N ASP A 468 " --> pdb=" O PRO A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 505 through 527 Processing helix chain 'A' and resid 700 through 714 Processing helix chain 'A' and resid 755 through 765 removed outlier: 3.624A pdb=" N ALA A 759 " --> pdb=" O LYS A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 845 Processing helix chain 'A' and resid 851 through 855 removed outlier: 3.891A pdb=" N ALA A 854 " --> pdb=" O ASN A 851 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 855 " --> pdb=" O ILE A 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 851 through 855' Processing helix chain 'A' and resid 914 through 916 No H-bonds generated for 'chain 'A' and resid 914 through 916' Processing helix chain 'A' and resid 929 through 932 Processing helix chain 'A' and resid 933 through 947 Processing helix chain 'A' and resid 950 through 955 Processing helix chain 'A' and resid 1019 through 1023 removed outlier: 3.707A pdb=" N LEU A1022 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1040 Processing sheet with id=AA1, first strand: chain 'A' and resid 729 through 731 removed outlier: 3.956A pdb=" N SER A 531 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ALA A 20 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE A 33 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 347 Processing sheet with id=AA4, first strand: chain 'A' and resid 890 through 894 Processing sheet with id=AA5, first strand: chain 'A' and resid 959 through 962 removed outlier: 4.674A pdb=" N VAL A 959 " --> pdb=" O VAL A 972 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 985 through 987 Processing sheet with id=AA7, first strand: chain 'A' and resid 1010 through 1017 removed outlier: 3.510A pdb=" N ARG A1001 " --> pdb=" O ILE A1016 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE A1002 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A1052 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A1004 " --> pdb=" O LYS A1050 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1029 through 1030 removed outlier: 3.705A pdb=" N ARG A1041 " --> pdb=" O LEU A1030 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1105 through 1109 removed outlier: 5.054A pdb=" N LYS A1107 " --> pdb=" O LEU A1097 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU A1097 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR A1094 " --> pdb=" O ALA A1088 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ALA A1088 " --> pdb=" O THR A1094 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR A1096 " --> pdb=" O ALA A1086 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A1058 " --> pdb=" O TYR A1120 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A1116 " --> pdb=" O LYS A1062 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1068 through 1070 288 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 155 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1895 1.33 - 1.45: 3017 1.45 - 1.57: 4990 1.57 - 1.69: 282 1.69 - 1.81: 32 Bond restraints: 10216 Sorted by residual: bond pdb=" N9 A B 59 " pdb=" C4 A B 59 " ideal model delta sigma weight residual 1.374 1.350 0.024 6.00e-03 2.78e+04 1.66e+01 bond pdb=" C3' DT D 7 " pdb=" C2' DT D 7 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.77e+00 bond pdb=" C1' DT C 22 " pdb=" N1 DT C 22 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.71e+00 bond pdb=" C5' DG C 18 " pdb=" C4' DG C 18 " ideal model delta sigma weight residual 1.512 1.529 -0.017 7.00e-03 2.04e+04 5.83e+00 bond pdb=" C3' DC C 14 " pdb=" C2' DC C 14 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.75e+00 ... (remaining 10211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 13219 1.25 - 2.50: 940 2.50 - 3.75: 254 3.75 - 4.99: 20 4.99 - 6.24: 6 Bond angle restraints: 14439 Sorted by residual: angle pdb=" N1 C B 91 " pdb=" C2 C B 91 " pdb=" O2 C B 91 " ideal model delta sigma weight residual 118.90 121.94 -3.04 6.00e-01 2.78e+00 2.57e+01 angle pdb=" O4' DG D 1 " pdb=" C4' DG D 1 " pdb=" C3' DG D 1 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" O4' DA D 0 " pdb=" C4' DA D 0 " pdb=" C3' DA D 0 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" O4' C B 64 " pdb=" C1' C B 64 " pdb=" N1 C B 64 " ideal model delta sigma weight residual 108.20 111.80 -3.60 8.00e-01 1.56e+00 2.03e+01 angle pdb=" N3 DT C 31 " pdb=" C4 DT C 31 " pdb=" O4 DT C 31 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 14434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.00: 5473 29.00 - 58.00: 573 58.00 - 87.00: 128 87.00 - 116.00: 4 116.00 - 145.00: 1 Dihedral angle restraints: 6179 sinusoidal: 3745 harmonic: 2434 Sorted by residual: dihedral pdb=" CA ASP A 42 " pdb=" C ASP A 42 " pdb=" N LYS A 43 " pdb=" CA LYS A 43 " ideal model delta harmonic sigma weight residual 180.00 154.89 25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ASP A 253 " pdb=" C ASP A 253 " pdb=" N ASP A 254 " pdb=" CA ASP A 254 " ideal model delta harmonic sigma weight residual 180.00 157.67 22.33 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LYS A 48 " pdb=" C LYS A 48 " pdb=" N THR A 49 " pdb=" CA THR A 49 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 6176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1060 0.037 - 0.074: 365 0.074 - 0.112: 151 0.112 - 0.149: 116 0.149 - 0.186: 6 Chirality restraints: 1698 Sorted by residual: chirality pdb=" C1' G B 78 " pdb=" O4' G B 78 " pdb=" C2' G B 78 " pdb=" N9 G B 78 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" C1' G B 88 " pdb=" O4' G B 88 " pdb=" C2' G B 88 " pdb=" N9 G B 88 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" C3' G B 45 " pdb=" C4' G B 45 " pdb=" O3' G B 45 " pdb=" C2' G B 45 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 1695 not shown) Planarity restraints: 1325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 957 " -0.044 5.00e-02 4.00e+02 6.69e-02 7.17e+00 pdb=" N PRO A 958 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 958 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 958 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 88 " 0.032 2.00e-02 2.50e+03 1.33e-02 5.31e+00 pdb=" N9 G B 88 " -0.029 2.00e-02 2.50e+03 pdb=" C8 G B 88 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G B 88 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G B 88 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 88 " 0.000 2.00e-02 2.50e+03 pdb=" O6 G B 88 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G B 88 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 88 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G B 88 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G B 88 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G B 88 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 201 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" CG ASN A 201 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 201 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 201 " 0.012 2.00e-02 2.50e+03 ... (remaining 1322 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2074 2.79 - 3.32: 7802 3.32 - 3.85: 17883 3.85 - 4.37: 21278 4.37 - 4.90: 32095 Nonbonded interactions: 81132 Sorted by model distance: nonbonded pdb=" OE1 GLN A 330 " pdb=" NH2 ARG A 333 " model vdw 2.264 3.120 nonbonded pdb=" OH TYR A 167 " pdb=" OE2 GLU A 177 " model vdw 2.290 3.040 nonbonded pdb=" OD1 ASP A 965 " pdb=" OG SER A 967 " model vdw 2.300 3.040 nonbonded pdb=" OD1 ASP A 473 " pdb=" N VAL A 474 " model vdw 2.331 3.120 nonbonded pdb=" OD1 ASP A 254 " pdb=" NH1 ARG A 273 " model vdw 2.342 3.120 ... (remaining 81127 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: 2.980 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.620 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10216 Z= 0.371 Angle : 0.743 6.242 14439 Z= 0.592 Chirality : 0.053 0.186 1698 Planarity : 0.005 0.067 1325 Dihedral : 20.969 144.996 4611 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.28 % Allowed : 18.40 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.29), residues: 824 helix: 1.31 (0.29), residues: 321 sheet: 0.15 (0.47), residues: 115 loop : -0.52 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 65 TYR 0.012 0.002 TYR A 341 PHE 0.015 0.002 PHE A 300 TRP 0.005 0.001 TRP A 420 HIS 0.006 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.37 (10216) covalent geometry : angle 0.74318 / 0.59 (14439) hydrogen bonds : bond 0.13109 / 8.19 ( 443) hydrogen bonds : angle 4.90506 / 3.68 ( 1110) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.196 Fit side-chains REVERT: A 192 LYS cc_start: 0.7566 (mtmm) cc_final: 0.6434 (pttt) REVERT: A 236 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: A 386 LYS cc_start: 0.7769 (mtmm) cc_final: 0.7086 (mptt) REVERT: A 846 ASP cc_start: 0.6510 (m-30) cc_final: 0.6255 (m-30) REVERT: A 1107 LYS cc_start: 0.8500 (mttt) cc_final: 0.8249 (tttm) outliers start: 2 outliers final: 1 residues processed: 83 average time/residue: 0.7264 time to fit residues: 63.3328 Evaluate side-chains 79 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 236 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.0570 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN A1028 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.167622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122255 restraints weight = 7760.914| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.25 r_work: 0.3168 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10216 Z= 0.182 Angle : 0.621 6.315 14439 Z= 0.359 Chirality : 0.045 0.228 1698 Planarity : 0.005 0.056 1325 Dihedral : 21.066 146.196 2938 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.63 % Allowed : 16.60 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.61 (0.29), residues: 824 helix: 1.66 (0.30), residues: 318 sheet: 0.21 (0.47), residues: 115 loop : -0.55 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 65 TYR 0.012 0.001 TYR A 341 PHE 0.014 0.002 PHE A 300 TRP 0.005 0.001 TRP A 420 HIS 0.005 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (10216) covalent geometry : angle 0.62061 / 0.36 (14439) hydrogen bonds : bond 0.06981 / 4.73 ( 443) hydrogen bonds : angle 4.13027 / 3.06 ( 1110) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.206 Fit side-chains REVERT: A 191 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6566 (pptt) REVERT: A 846 ASP cc_start: 0.6665 (m-30) cc_final: 0.6094 (m-30) REVERT: A 1133 LYS cc_start: 0.8374 (tptp) cc_final: 0.7811 (tmmt) outliers start: 19 outliers final: 9 residues processed: 95 average time/residue: 0.7068 time to fit residues: 70.3881 Evaluate side-chains 86 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 89 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 chunk 17 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1028 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.167484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120039 restraints weight = 7814.815| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.35 r_work: 0.3163 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10216 Z= 0.182 Angle : 0.620 6.547 14439 Z= 0.356 Chirality : 0.045 0.231 1698 Planarity : 0.005 0.049 1325 Dihedral : 20.966 146.336 2935 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.04 % Allowed : 16.74 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.29), residues: 824 helix: 1.69 (0.29), residues: 319 sheet: 0.26 (0.47), residues: 115 loop : -0.63 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 892 TYR 0.018 0.002 TYR A 341 PHE 0.014 0.002 PHE A 300 TRP 0.006 0.001 TRP A 420 HIS 0.003 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (10216) covalent geometry : angle 0.62041 / 0.36 (14439) hydrogen bonds : bond 0.06751 / 4.60 ( 443) hydrogen bonds : angle 4.03168 / 2.99 ( 1110) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.194 Fit side-chains REVERT: A 156 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: A 236 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: A 384 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6827 (tm-30) REVERT: A 525 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8118 (tptm) REVERT: A 846 ASP cc_start: 0.6679 (m-30) cc_final: 0.6144 (m-30) REVERT: A 973 ARG cc_start: 0.8858 (mtt180) cc_final: 0.8627 (mpp80) REVERT: A 995 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8303 (mt-10) REVERT: A 1133 LYS cc_start: 0.8341 (tptp) cc_final: 0.7789 (tmmt) outliers start: 22 outliers final: 10 residues processed: 97 average time/residue: 0.7180 time to fit residues: 73.3054 Evaluate side-chains 89 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1068 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 94 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN A1028 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.167091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119660 restraints weight = 7846.606| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.18 r_work: 0.3173 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10216 Z= 0.189 Angle : 0.629 6.596 14439 Z= 0.360 Chirality : 0.045 0.233 1698 Planarity : 0.005 0.045 1325 Dihedral : 20.976 146.068 2935 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.32 % Allowed : 16.60 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.29), residues: 824 helix: 1.57 (0.29), residues: 325 sheet: 0.24 (0.47), residues: 115 loop : -0.63 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 892 TYR 0.019 0.002 TYR A 341 PHE 0.015 0.002 PHE A 451 TRP 0.006 0.001 TRP A 420 HIS 0.003 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (10216) covalent geometry : angle 0.62947 / 0.36 (14439) hydrogen bonds : bond 0.06824 / 4.65 ( 443) hydrogen bonds : angle 4.02474 / 2.98 ( 1110) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.205 Fit side-chains REVERT: A 156 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: A 162 MET cc_start: 0.7050 (mmp) cc_final: 0.6730 (mmm) REVERT: A 236 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: A 384 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6967 (tm-30) REVERT: A 525 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8110 (tptm) REVERT: A 846 ASP cc_start: 0.6727 (m-30) cc_final: 0.6254 (m-30) REVERT: A 973 ARG cc_start: 0.8851 (mtt180) cc_final: 0.8612 (mpp80) REVERT: A 995 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: A 1133 LYS cc_start: 0.8341 (tptp) cc_final: 0.7794 (tmmt) outliers start: 24 outliers final: 14 residues processed: 97 average time/residue: 0.6508 time to fit residues: 66.4614 Evaluate side-chains 93 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1134 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 41 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN A1028 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.168045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121149 restraints weight = 7777.475| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.37 r_work: 0.3180 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10216 Z= 0.160 Angle : 0.582 6.457 14439 Z= 0.338 Chirality : 0.043 0.231 1698 Planarity : 0.004 0.042 1325 Dihedral : 20.927 146.580 2935 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.46 % Allowed : 16.87 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.29), residues: 824 helix: 1.72 (0.29), residues: 325 sheet: 0.26 (0.47), residues: 115 loop : -0.61 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 509 TYR 0.019 0.001 TYR A 341 PHE 0.013 0.002 PHE A 300 TRP 0.006 0.001 TRP A 420 HIS 0.003 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (10216) covalent geometry : angle 0.58249 / 0.34 (14439) hydrogen bonds : bond 0.06192 / 4.22 ( 443) hydrogen bonds : angle 3.94968 / 2.93 ( 1110) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.177 Fit side-chains REVERT: A 156 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.6941 (tm-30) REVERT: A 172 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: A 192 LYS cc_start: 0.7755 (mtmm) cc_final: 0.6324 (pttt) REVERT: A 236 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: A 384 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: A 432 THR cc_start: 0.7862 (m) cc_final: 0.7603 (m) REVERT: A 509 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6671 (ttp-170) REVERT: A 846 ASP cc_start: 0.6679 (m-30) cc_final: 0.6231 (m-30) REVERT: A 973 ARG cc_start: 0.8832 (mtt180) cc_final: 0.8494 (mtm-85) REVERT: A 995 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8244 (mt-10) REVERT: A 1133 LYS cc_start: 0.8319 (tptp) cc_final: 0.7722 (tmmt) outliers start: 25 outliers final: 16 residues processed: 99 average time/residue: 0.6842 time to fit residues: 71.2928 Evaluate side-chains 98 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 30 optimal weight: 9.9990 chunk 39 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN A1028 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.170942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.123954 restraints weight = 7891.366| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.38 r_work: 0.3219 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10216 Z= 0.121 Angle : 0.514 6.227 14439 Z= 0.303 Chirality : 0.039 0.227 1698 Planarity : 0.004 0.038 1325 Dihedral : 20.863 147.145 2935 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.18 % Allowed : 17.01 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.90 (0.29), residues: 824 helix: 1.97 (0.29), residues: 325 sheet: 0.57 (0.49), residues: 111 loop : -0.58 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 892 TYR 0.017 0.001 TYR A 341 PHE 0.011 0.002 PHE A 836 TRP 0.004 0.001 TRP A 420 HIS 0.003 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.12 (10216) covalent geometry : angle 0.51401 / 0.30 (14439) hydrogen bonds : bond 0.05023 / 3.44 ( 443) hydrogen bonds : angle 3.80621 / 2.83 ( 1110) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.202 Fit side-chains REVERT: A 192 LYS cc_start: 0.7709 (mtmm) cc_final: 0.6370 (pttt) REVERT: A 236 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: A 384 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6800 (tm-30) REVERT: A 432 THR cc_start: 0.7788 (m) cc_final: 0.7512 (m) REVERT: A 846 ASP cc_start: 0.6622 (m-30) cc_final: 0.6036 (m-30) REVERT: A 995 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8262 (mt-10) outliers start: 23 outliers final: 16 residues processed: 96 average time/residue: 0.7592 time to fit residues: 76.7369 Evaluate side-chains 96 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 150 LYS Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 33 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN A1028 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.167394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120355 restraints weight = 7757.725| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.37 r_work: 0.3171 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10216 Z= 0.191 Angle : 0.625 6.894 14439 Z= 0.355 Chirality : 0.045 0.232 1698 Planarity : 0.005 0.039 1325 Dihedral : 20.888 146.462 2935 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.77 % Allowed : 17.84 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.29), residues: 824 helix: 1.75 (0.29), residues: 325 sheet: 0.32 (0.48), residues: 115 loop : -0.59 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 892 TYR 0.021 0.002 TYR A 341 PHE 0.015 0.003 PHE A 300 TRP 0.006 0.001 TRP A 420 HIS 0.004 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (10216) covalent geometry : angle 0.62507 / 0.36 (14439) hydrogen bonds : bond 0.06662 / 4.54 ( 443) hydrogen bonds : angle 3.96819 / 2.94 ( 1110) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.310 Fit side-chains REVERT: A 192 LYS cc_start: 0.7726 (mtmm) cc_final: 0.6326 (pttt) REVERT: A 236 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: A 384 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6875 (tm-30) REVERT: A 432 THR cc_start: 0.7814 (m) cc_final: 0.7549 (m) REVERT: A 846 ASP cc_start: 0.6665 (m-30) cc_final: 0.6194 (m-30) REVERT: A 995 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8293 (mt-10) REVERT: A 1133 LYS cc_start: 0.8331 (tptp) cc_final: 0.7726 (tmmt) outliers start: 20 outliers final: 15 residues processed: 95 average time/residue: 0.8066 time to fit residues: 80.5170 Evaluate side-chains 97 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 74 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 33 optimal weight: 0.0570 chunk 64 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN A1028 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.166618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119268 restraints weight = 7797.997| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.40 r_work: 0.3143 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10216 Z= 0.211 Angle : 0.663 7.358 14439 Z= 0.374 Chirality : 0.047 0.235 1698 Planarity : 0.005 0.040 1325 Dihedral : 20.901 146.584 2935 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.18 % Allowed : 18.12 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.28), residues: 824 helix: 1.54 (0.29), residues: 325 sheet: 0.27 (0.47), residues: 115 loop : -0.63 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 892 TYR 0.023 0.002 TYR A 341 PHE 0.018 0.003 PHE A 451 TRP 0.007 0.001 TRP A 420 HIS 0.003 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (10216) covalent geometry : angle 0.66251 / 0.37 (14439) hydrogen bonds : bond 0.07137 / 4.86 ( 443) hydrogen bonds : angle 4.06301 / 3.01 ( 1110) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.278 Fit side-chains REVERT: A 156 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: A 192 LYS cc_start: 0.7776 (mtmm) cc_final: 0.6394 (pttt) REVERT: A 236 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: A 384 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6932 (tm-30) REVERT: A 392 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6656 (ttm110) REVERT: A 432 THR cc_start: 0.7851 (m) cc_final: 0.7600 (m) REVERT: A 846 ASP cc_start: 0.6782 (m-30) cc_final: 0.6285 (m-30) REVERT: A 964 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7724 (mtpt) REVERT: A 995 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8300 (mt-10) REVERT: A 1133 LYS cc_start: 0.8357 (tptp) cc_final: 0.7753 (tmmt) outliers start: 23 outliers final: 16 residues processed: 97 average time/residue: 0.7711 time to fit residues: 78.7468 Evaluate side-chains 99 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1134 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 91 optimal weight: 7.9990 chunk 9 optimal weight: 0.0370 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 65 optimal weight: 0.0050 chunk 26 optimal weight: 0.7980 overall best weight: 0.4672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN A1028 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.171728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127444 restraints weight = 7817.509| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.30 r_work: 0.3228 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10216 Z= 0.116 Angle : 0.517 7.505 14439 Z= 0.305 Chirality : 0.038 0.227 1698 Planarity : 0.004 0.039 1325 Dihedral : 20.820 147.594 2935 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.35 % Allowed : 18.95 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.29), residues: 824 helix: 2.12 (0.30), residues: 318 sheet: 0.32 (0.46), residues: 121 loop : -0.61 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 892 TYR 0.017 0.001 TYR A 341 PHE 0.011 0.001 PHE A 836 TRP 0.004 0.001 TRP A 420 HIS 0.004 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.12 (10216) covalent geometry : angle 0.51686 / 0.30 (14439) hydrogen bonds : bond 0.04921 / 3.37 ( 443) hydrogen bonds : angle 3.80529 / 2.83 ( 1110) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.295 Fit side-chains REVERT: A 192 LYS cc_start: 0.7708 (mtmm) cc_final: 0.6322 (pttt) REVERT: A 236 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: A 306 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7622 (mp) REVERT: A 384 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6919 (tm-30) REVERT: A 432 THR cc_start: 0.7775 (m) cc_final: 0.7511 (m) REVERT: A 846 ASP cc_start: 0.6671 (m-30) cc_final: 0.6110 (m-30) REVERT: A 995 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8250 (mt-10) REVERT: A 1133 LYS cc_start: 0.8298 (tptp) cc_final: 0.7681 (tmmt) outliers start: 17 outliers final: 12 residues processed: 97 average time/residue: 0.6990 time to fit residues: 71.3142 Evaluate side-chains 94 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 36 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 77 optimal weight: 0.0370 chunk 25 optimal weight: 0.0020 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 overall best weight: 0.9268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN A1028 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.170619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127355 restraints weight = 7745.621| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.13 r_work: 0.3214 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10216 Z= 0.125 Angle : 0.521 6.540 14439 Z= 0.307 Chirality : 0.039 0.226 1698 Planarity : 0.004 0.039 1325 Dihedral : 20.790 147.158 2935 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.35 % Allowed : 18.81 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.29), residues: 824 helix: 2.13 (0.30), residues: 319 sheet: 0.39 (0.47), residues: 115 loop : -0.56 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 892 TYR 0.018 0.001 TYR A 341 PHE 0.011 0.002 PHE A 300 TRP 0.004 0.001 TRP A 420 HIS 0.004 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (10216) covalent geometry : angle 0.52142 / 0.31 (14439) hydrogen bonds : bond 0.05076 / 3.47 ( 443) hydrogen bonds : angle 3.79079 / 2.82 ( 1110) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.264 Fit side-chains REVERT: A 192 LYS cc_start: 0.7737 (mtmm) cc_final: 0.6362 (pttt) REVERT: A 236 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: A 306 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7658 (mp) REVERT: A 384 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: A 432 THR cc_start: 0.7784 (m) cc_final: 0.7516 (m) REVERT: A 846 ASP cc_start: 0.6711 (m-30) cc_final: 0.6112 (m-30) REVERT: A 995 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: A 1133 LYS cc_start: 0.8300 (tptp) cc_final: 0.7714 (tmmt) outliers start: 17 outliers final: 12 residues processed: 91 average time/residue: 0.6503 time to fit residues: 62.5243 Evaluate side-chains 93 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 995 GLU Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 91 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN A1028 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.170308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122813 restraints weight = 7780.656| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.33 r_work: 0.3223 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10216 Z= 0.130 Angle : 0.530 6.459 14439 Z= 0.310 Chirality : 0.039 0.225 1698 Planarity : 0.004 0.043 1325 Dihedral : 20.773 147.190 2935 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.63 % Allowed : 18.40 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.29), residues: 824 helix: 2.11 (0.30), residues: 319 sheet: 0.40 (0.47), residues: 115 loop : -0.57 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 892 TYR 0.018 0.001 TYR A 341 PHE 0.012 0.002 PHE A 300 TRP 0.004 0.001 TRP A 420 HIS 0.004 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (10216) covalent geometry : angle 0.52986 / 0.31 (14439) hydrogen bonds : bond 0.05203 / 3.56 ( 443) hydrogen bonds : angle 3.79938 / 2.82 ( 1110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3635.77 seconds wall clock time: 62 minutes 25.09 seconds (3745.09 seconds total)