Starting phenix.real_space_refine on Wed Aug 5 12:48:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21ea_67606/08_2026/21ea_67606.cif Found real_map, /net/cci-nas-00/data/ceres_data/21ea_67606/08_2026/21ea_67606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21ea_67606/08_2026/21ea_67606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21ea_67606/08_2026/21ea_67606.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21ea_67606/08_2026/21ea_67606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21ea_67606/08_2026/21ea_67606.map" } resolution = 2.65 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= 0.063 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 145 5.49 5 S 20 5.16 5 C 5634 2.51 5 N 1765 2.21 5 O 2186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 9750 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 839, 6702 Classifications: {'peptide': 839} Link IDs: {'PTRANS': 33, 'TRANS': 805} Chain breaks: 10 Chain: "B" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2075 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 45, 'rna3p_pyr': 46} Link IDs: {'rna2p': 7, 'rna3p': 90} Chain breaks: 3 Chain: "C" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 726 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "D" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 247 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 1.84, per 1000 atoms: 0.19 Number of scatterers: 9750 At special positions: 0 Unit cell: (86.1, 111.3, 122.85, 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 145 15.00 O 2186 8.00 N 1765 7.00 C 5634 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: 0.64 Conformation dependent library (CDL) restraints added in 161.6 milliseconds 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 39.3% alpha, 13.7% beta 56 base pairs and 99 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 54 through 84 Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 118 through 132 removed outlier: 3.779A pdb=" N ARG A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 166 removed outlier: 3.700A pdb=" N MET A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 179 removed outlier: 3.919A pdb=" N THR A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.698A pdb=" N TYR A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 385 through 399 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 467 Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 505 through 527 removed outlier: 3.603A pdb=" N ARG A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 716 Processing helix chain 'A' and resid 755 through 766 removed outlier: 3.920A pdb=" N ALA A 759 " --> pdb=" O LYS A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 844 removed outlier: 3.592A pdb=" N ALA A 842 " --> pdb=" O ASP A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 857 removed outlier: 3.616A pdb=" N LEU A 857 " --> pdb=" O ALA A 854 " (cutoff:3.500A) 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 1021 No H-bonds generated for 'chain 'A' and resid 1019 through 1021' Processing helix chain 'A' and resid 1036 through 1040 removed outlier: 3.604A pdb=" N TRP A1040 " --> pdb=" O TYR A1037 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 37 removed outlier: 6.461A pdb=" N ILE A 33 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA A 20 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A 531 " --> pdb=" O TYR A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 347 removed outlier: 6.788A pdb=" N ILE A 346 " --> pdb=" O PHE A 382 " (cutoff:3.500A) 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: 4.618A 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: 3.549A pdb=" N ARG A1001 " --> pdb=" O ILE A1016 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A1002 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER A1052 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 6.808A 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: 3.884A 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: 5.367A pdb=" N LEU A1095 " --> pdb=" O GLY A1108 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG A1098 " --> pdb=" O PHE A1085 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N PHE A1085 " --> pdb=" O ARG A1098 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA A1058 " --> pdb=" O TYR A1120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1068 through 1071 278 hydrogen bonds defined for protein. 789 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 268 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 99 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 0.93 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: 1923 1.33 - 1.45: 2992 1.45 - 1.57: 4989 1.57 - 1.69: 284 1.69 - 1.81: 32 Bond restraints: 10220 Sorted by residual: bond pdb=" N9 A B 59 " pdb=" C4 A B 59 " ideal model delta sigma weight residual 1.374 1.352 0.022 6.00e-03 2.78e+04 1.29e+01 bond pdb=" C3' DC D 9 " pdb=" C2' DC D 9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.92e+00 bond pdb=" N ASP A 847 " pdb=" CA ASP A 847 " ideal model delta sigma weight residual 1.462 1.488 -0.026 8.50e-03 1.38e+04 9.69e+00 bond pdb=" C3' DT C -1 " pdb=" C2' DT C -1 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.47e+00 bond pdb=" CA SER A 845 " pdb=" CB SER A 845 " ideal model delta sigma weight residual 1.536 1.499 0.037 1.46e-02 4.69e+03 6.48e+00 ... (remaining 10215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 13857 1.97 - 3.93: 568 3.93 - 5.90: 19 5.90 - 7.87: 3 7.87 - 9.83: 2 Bond angle restraints: 14449 Sorted by residual: angle pdb=" O4' DG C 15 " pdb=" C4' DG C 15 " pdb=" C3' DG C 15 " ideal model delta sigma weight residual 106.00 102.68 3.32 6.00e-01 2.78e+00 3.07e+01 angle pdb=" N ASP A 846 " pdb=" CA ASP A 846 " pdb=" C ASP A 846 " ideal model delta sigma weight residual 113.50 107.45 6.05 1.23e+00 6.61e-01 2.42e+01 angle pdb=" N3 DT D 5 " pdb=" C4 DT D 5 " pdb=" O4 DT D 5 " ideal model delta sigma weight residual 119.90 122.84 -2.94 6.00e-01 2.78e+00 2.40e+01 angle pdb=" C1' C B 91 " pdb=" N1 C B 91 " pdb=" C2 C B 91 " ideal model delta sigma weight residual 118.80 123.95 -5.15 1.10e+00 8.26e-01 2.19e+01 angle pdb=" N3 DT C -1 " pdb=" C4 DT C -1 " pdb=" O4 DT C -1 " ideal model delta sigma weight residual 119.90 122.67 -2.77 6.00e-01 2.78e+00 2.12e+01 ... (remaining 14444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.78: 5464 28.78 - 57.57: 581 57.57 - 86.35: 131 86.35 - 115.13: 5 115.13 - 143.91: 1 Dihedral angle restraints: 6182 sinusoidal: 3755 harmonic: 2427 Sorted by residual: dihedral pdb=" C4' G B 45 " pdb=" C3' G B 45 " pdb=" O3' G B 45 " pdb=" P A B 46 " ideal model delta sinusoidal sigma weight residual 220.00 76.09 143.91 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CA LEU A 7 " pdb=" C LEU A 7 " pdb=" N ALA A 8 " pdb=" CA ALA A 8 " ideal model delta harmonic sigma weight residual 180.00 161.61 18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" O4' C B 1 " pdb=" C1' C B 1 " pdb=" N1 C B 1 " pdb=" C2 C B 1 " ideal model delta sinusoidal sigma weight residual -160.00 -114.06 -45.94 1 1.50e+01 4.44e-03 1.30e+01 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1089 0.038 - 0.076: 359 0.076 - 0.115: 140 0.115 - 0.153: 111 0.153 - 0.191: 5 Chirality restraints: 1704 Sorted by residual: 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 2.28 0.19 2.00e-01 2.50e+01 9.12e-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 -2.29 -0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" C1' C B 63 " pdb=" O4' C B 63 " pdb=" C2' C B 63 " pdb=" N1 C B 63 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 1701 not shown) Planarity restraints: 1319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 88 " 0.032 2.00e-02 2.50e+03 1.37e-02 5.61e+00 pdb=" N9 G B 88 " -0.032 2.00e-02 2.50e+03 pdb=" C8 G B 88 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G B 88 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 88 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 88 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G B 88 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G B 88 " 0.000 2.00e-02 2.50e+03 pdb=" C2 G B 88 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G B 88 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G B 88 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G B 88 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 109 " -0.024 2.00e-02 2.50e+03 1.32e-02 3.90e+00 pdb=" N1 C B 109 " 0.030 2.00e-02 2.50e+03 pdb=" C2 C B 109 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C B 109 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C B 109 " -0.000 2.00e-02 2.50e+03 pdb=" C4 C B 109 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C B 109 " -0.007 2.00e-02 2.50e+03 pdb=" C5 C B 109 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C B 109 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 63 " -0.023 2.00e-02 2.50e+03 1.10e-02 2.71e+00 pdb=" N1 C B 63 " 0.021 2.00e-02 2.50e+03 pdb=" C2 C B 63 " 0.006 2.00e-02 2.50e+03 pdb=" O2 C B 63 " 0.002 2.00e-02 2.50e+03 pdb=" N3 C B 63 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C B 63 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C B 63 " -0.007 2.00e-02 2.50e+03 pdb=" C5 C B 63 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C B 63 " 0.006 2.00e-02 2.50e+03 ... (remaining 1316 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1613 2.77 - 3.30: 7979 3.30 - 3.83: 17541 3.83 - 4.37: 21479 4.37 - 4.90: 32651 Nonbonded interactions: 81263 Sorted by model distance: nonbonded pdb=" O TYR A 206 " pdb=" OG1 THR A 209 " model vdw 2.232 3.040 nonbonded pdb=" O2' G B 45 " pdb=" OP1 A B 46 " model vdw 2.262 3.040 nonbonded pdb=" ND2 ASN A 851 " pdb=" O ILE A 866 " model vdw 2.304 3.120 nonbonded pdb=" NZ LYS A 192 " pdb=" OP1 U B 33 " model vdw 2.324 3.120 nonbonded pdb=" NZ LYS A 976 " pdb=" OP1 U B 49 " model vdw 2.334 3.120 ... (remaining 81258 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.010 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.690 Find NCS groups from input model: 0.040 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:8.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 0.037 10220 Z= 0.363 Angle : 0.733 9.833 14449 Z= 0.590 Chirality : 0.053 0.191 1704 Planarity : 0.004 0.032 1319 Dihedral : 21.138 143.913 4616 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.42 % Allowed : 21.36 % Favored : 78.22 % 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: -0.03 (0.28), residues: 817 helix: 1.45 (0.30), residues: 306 sheet: -0.76 (0.46), residues: 107 loop : -0.96 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 973 TYR 0.013 0.001 TYR A 960 PHE 0.015 0.002 PHE A 41 TRP 0.005 0.001 TRP A 16 HIS 0.003 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.36 (10220) covalent geometry : angle 0.73336 / 0.59 (14449) hydrogen bonds : bond 0.09764 / 7.07 ( 418) hydrogen bonds : angle 4.88890 / 3.34 ( 1057) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.287 Fit side-chains REVERT: A 140 LYS cc_start: 0.6668 (tttp) cc_final: 0.5407 (ptpp) REVERT: A 917 LYS cc_start: 0.8162 (mttp) cc_final: 0.7706 (mmtm) REVERT: A 1065 ARG cc_start: 0.6598 (mpt180) cc_final: 0.6064 (ptt-90) outliers start: 3 outliers final: 4 residues processed: 94 average time/residue: 0.6978 time to fit residues: 69.1868 Evaluate side-chains 87 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 1091 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 74 optimal weight: 0.0050 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.157270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118503 restraints weight = 9239.350| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.32 r_work: 0.3216 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10220 Z= 0.117 Angle : 0.506 8.155 14449 Z= 0.300 Chirality : 0.038 0.236 1704 Planarity : 0.004 0.028 1319 Dihedral : 21.112 144.801 2951 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.02 % Allowed : 18.03 % Favored : 77.95 % 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: 0.36 (0.29), residues: 817 helix: 1.90 (0.31), residues: 307 sheet: -0.63 (0.47), residues: 97 loop : -0.84 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 139 TYR 0.007 0.001 TYR A 960 PHE 0.009 0.001 PHE A 41 TRP 0.004 0.001 TRP A 415 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.12 (10220) covalent geometry : angle 0.50592 / 0.30 (14449) hydrogen bonds : bond 0.05075 / 3.75 ( 418) hydrogen bonds : angle 4.09303 / 2.87 ( 1057) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.302 Fit side-chains REVERT: A 140 LYS cc_start: 0.6743 (tttp) cc_final: 0.5326 (ptpp) REVERT: A 720 GLU cc_start: 0.5701 (OUTLIER) cc_final: 0.5097 (mt-10) REVERT: A 917 LYS cc_start: 0.8395 (mttp) cc_final: 0.7945 (mmtm) REVERT: A 1065 ARG cc_start: 0.6691 (mpt180) cc_final: 0.6106 (mtm180) outliers start: 29 outliers final: 16 residues processed: 111 average time/residue: 0.6610 time to fit residues: 77.6953 Evaluate side-chains 103 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1091 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.150639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.114093 restraints weight = 9256.537| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.71 r_work: 0.3084 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 10220 Z= 0.303 Angle : 0.708 9.687 14449 Z= 0.387 Chirality : 0.051 0.252 1704 Planarity : 0.006 0.055 1319 Dihedral : 21.156 146.275 2949 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.30 % Allowed : 18.59 % Favored : 77.12 % 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: -0.19 (0.28), residues: 817 helix: 1.31 (0.29), residues: 306 sheet: -0.76 (0.47), residues: 97 loop : -1.07 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 39 TYR 0.014 0.002 TYR A 960 PHE 0.019 0.003 PHE A 41 TRP 0.011 0.002 TRP A 16 HIS 0.006 0.002 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.30 (10220) covalent geometry : angle 0.70823 / 0.39 (14449) hydrogen bonds : bond 0.07469 / 5.40 ( 418) hydrogen bonds : angle 4.30645 / 3.03 ( 1057) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.271 Fit side-chains REVERT: A 140 LYS cc_start: 0.7099 (tttp) cc_final: 0.5221 (ptpp) REVERT: A 720 GLU cc_start: 0.5862 (OUTLIER) cc_final: 0.5287 (mt-10) REVERT: A 917 LYS cc_start: 0.8502 (mttp) cc_final: 0.8231 (mmtp) REVERT: A 1065 ARG cc_start: 0.6916 (mpt180) cc_final: 0.6107 (mtm180) outliers start: 31 outliers final: 21 residues processed: 110 average time/residue: 0.5296 time to fit residues: 61.8474 Evaluate side-chains 108 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1091 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 58 optimal weight: 0.0470 chunk 46 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116287 restraints weight = 9369.164| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.33 r_work: 0.3179 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10220 Z= 0.130 Angle : 0.518 8.908 14449 Z= 0.303 Chirality : 0.039 0.235 1704 Planarity : 0.004 0.031 1319 Dihedral : 21.070 145.587 2949 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.16 % Allowed : 18.72 % Favored : 77.12 % 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: 0.17 (0.29), residues: 817 helix: 1.73 (0.30), residues: 307 sheet: -0.73 (0.46), residues: 97 loop : -0.94 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 64 TYR 0.009 0.001 TYR A 341 PHE 0.010 0.001 PHE A 41 TRP 0.004 0.001 TRP A 415 HIS 0.003 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (10220) covalent geometry : angle 0.51753 / 0.30 (14449) hydrogen bonds : bond 0.05213 / 3.81 ( 418) hydrogen bonds : angle 4.05379 / 2.84 ( 1057) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.284 Fit side-chains REVERT: A 140 LYS cc_start: 0.7025 (tttp) cc_final: 0.5196 (ptpp) REVERT: A 395 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7105 (mp) REVERT: A 720 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.5145 (mt-10) REVERT: A 877 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8137 (mtt-85) REVERT: A 917 LYS cc_start: 0.8469 (mttp) cc_final: 0.8196 (mmtp) REVERT: A 1060 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8250 (tpp) REVERT: A 1065 ARG cc_start: 0.6789 (mpt180) cc_final: 0.6076 (mtm180) outliers start: 30 outliers final: 18 residues processed: 108 average time/residue: 0.6332 time to fit residues: 72.5122 Evaluate side-chains 105 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 ARG Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1016 ILE Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1091 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.152003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114332 restraints weight = 9350.439| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.31 r_work: 0.3139 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10220 Z= 0.229 Angle : 0.620 10.329 14449 Z= 0.346 Chirality : 0.045 0.239 1704 Planarity : 0.005 0.038 1319 Dihedral : 21.058 146.578 2949 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.72 % Allowed : 18.72 % Favored : 76.56 % 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: -0.06 (0.28), residues: 817 helix: 1.47 (0.30), residues: 307 sheet: -0.76 (0.46), residues: 97 loop : -1.04 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 39 TYR 0.012 0.002 TYR A 960 PHE 0.015 0.002 PHE A 41 TRP 0.008 0.002 TRP A 16 HIS 0.005 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.23 (10220) covalent geometry : angle 0.62011 / 0.35 (14449) hydrogen bonds : bond 0.06455 / 4.69 ( 418) hydrogen bonds : angle 4.14542 / 2.91 ( 1057) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.222 Fit side-chains REVERT: A 140 LYS cc_start: 0.7071 (tttp) cc_final: 0.5187 (ptpp) REVERT: A 720 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.5223 (mt-10) REVERT: A 877 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8154 (mtt-85) REVERT: A 917 LYS cc_start: 0.8485 (mttp) cc_final: 0.8212 (mmtp) REVERT: A 1060 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8113 (tpp) REVERT: A 1065 ARG cc_start: 0.6904 (mpt180) cc_final: 0.6091 (mtm180) outliers start: 34 outliers final: 20 residues processed: 112 average time/residue: 0.6852 time to fit residues: 81.3304 Evaluate side-chains 109 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 ARG Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1016 ILE Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1091 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.150732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114323 restraints weight = 9332.869| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.64 r_work: 0.3083 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10220 Z= 0.254 Angle : 0.667 11.487 14449 Z= 0.369 Chirality : 0.047 0.232 1704 Planarity : 0.006 0.051 1319 Dihedral : 21.041 147.177 2949 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.99 % Allowed : 18.72 % Favored : 76.28 % 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: -0.30 (0.28), residues: 817 helix: 1.24 (0.29), residues: 307 sheet: -0.91 (0.46), residues: 97 loop : -1.14 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 32 TYR 0.015 0.002 TYR A 960 PHE 0.015 0.003 PHE A1013 TRP 0.008 0.002 TRP A 16 HIS 0.005 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.25 (10220) covalent geometry : angle 0.66741 / 0.37 (14449) hydrogen bonds : bond 0.06998 / 5.08 ( 418) hydrogen bonds : angle 4.24300 / 2.99 ( 1057) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 0.387 Fit side-chains REVERT: A 115 ARG cc_start: 0.8557 (ttp80) cc_final: 0.8192 (ttp80) REVERT: A 140 LYS cc_start: 0.7153 (tttp) cc_final: 0.5269 (ptpp) REVERT: A 720 GLU cc_start: 0.5747 (OUTLIER) cc_final: 0.5133 (mt-10) REVERT: A 877 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8174 (mtt-85) REVERT: A 917 LYS cc_start: 0.8510 (mttp) cc_final: 0.8196 (mmtp) REVERT: A 1060 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8094 (tpp) REVERT: A 1065 ARG cc_start: 0.6916 (mpt180) cc_final: 0.6017 (mtm180) outliers start: 36 outliers final: 25 residues processed: 116 average time/residue: 0.6804 time to fit residues: 83.8317 Evaluate side-chains 114 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 877 ARG Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1016 ILE Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1075 LYS Chi-restraints excluded: chain A residue 1091 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.154618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116058 restraints weight = 9281.896| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.30 r_work: 0.3180 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10220 Z= 0.132 Angle : 0.520 9.480 14449 Z= 0.303 Chirality : 0.039 0.224 1704 Planarity : 0.004 0.034 1319 Dihedral : 20.926 147.279 2949 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.30 % Allowed : 19.97 % Favored : 75.73 % 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: 0.10 (0.29), residues: 817 helix: 1.72 (0.30), residues: 307 sheet: -0.85 (0.46), residues: 97 loop : -0.99 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.010 0.001 TYR A 960 PHE 0.010 0.001 PHE A 41 TRP 0.005 0.001 TRP A 75 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (10220) covalent geometry : angle 0.51963 / 0.30 (14449) hydrogen bonds : bond 0.05162 / 3.76 ( 418) hydrogen bonds : angle 4.03523 / 2.84 ( 1057) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.319 Fit side-chains REVERT: A 115 ARG cc_start: 0.8478 (ttp80) cc_final: 0.8099 (ttp80) REVERT: A 140 LYS cc_start: 0.7152 (tttp) cc_final: 0.5279 (ptpp) REVERT: A 350 LYS cc_start: 0.2825 (OUTLIER) cc_final: 0.0798 (pmtt) REVERT: A 395 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7114 (mp) REVERT: A 720 GLU cc_start: 0.5741 (OUTLIER) cc_final: 0.5127 (mt-10) REVERT: A 877 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8144 (mtt-85) REVERT: A 917 LYS cc_start: 0.8489 (mttp) cc_final: 0.8178 (mmtp) REVERT: A 1060 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8149 (tpp) REVERT: A 1065 ARG cc_start: 0.6824 (mpt180) cc_final: 0.5980 (mtm180) outliers start: 31 outliers final: 20 residues processed: 111 average time/residue: 0.7160 time to fit residues: 83.7335 Evaluate side-chains 111 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 ARG Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1016 ILE Chi-restraints excluded: chain A residue 1024 ARG Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1075 LYS Chi-restraints excluded: chain A residue 1091 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 45 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.3187 > 50:) chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.154264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.115722 restraints weight = 9286.883| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.30 r_work: 0.3171 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10220 Z= 0.144 Angle : 0.529 9.699 14449 Z= 0.304 Chirality : 0.039 0.228 1704 Planarity : 0.004 0.032 1319 Dihedral : 20.847 147.877 2949 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.74 % Allowed : 20.94 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.29), residues: 817 helix: 1.79 (0.30), residues: 307 sheet: -0.76 (0.46), residues: 97 loop : -0.93 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.009 0.001 TYR A 960 PHE 0.012 0.001 PHE A 41 TRP 0.006 0.001 TRP A 16 HIS 0.003 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (10220) covalent geometry : angle 0.52853 / 0.30 (14449) hydrogen bonds : bond 0.05234 / 3.81 ( 418) hydrogen bonds : angle 3.97429 / 2.79 ( 1057) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.231 Fit side-chains REVERT: A 115 ARG cc_start: 0.8477 (ttp80) cc_final: 0.8104 (ttp80) REVERT: A 140 LYS cc_start: 0.7163 (tttp) cc_final: 0.5260 (ptpp) REVERT: A 350 LYS cc_start: 0.2770 (OUTLIER) cc_final: 0.0755 (pmtt) REVERT: A 395 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7049 (mp) REVERT: A 720 GLU cc_start: 0.5778 (OUTLIER) cc_final: 0.5145 (mt-10) REVERT: A 917 LYS cc_start: 0.8495 (mttp) cc_final: 0.8174 (mmtp) REVERT: A 1060 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8203 (tpp) REVERT: A 1065 ARG cc_start: 0.6843 (mpt180) cc_final: 0.6002 (mtm180) REVERT: A 1075 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8101 (mmtp) outliers start: 27 outliers final: 19 residues processed: 111 average time/residue: 0.7185 time to fit residues: 84.1689 Evaluate side-chains 111 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1016 ILE Chi-restraints excluded: chain A residue 1024 ARG Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1075 LYS Chi-restraints excluded: chain A residue 1091 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 0.0050 chunk 49 optimal weight: 4.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.154262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.115705 restraints weight = 9253.043| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.30 r_work: 0.3170 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10220 Z= 0.150 Angle : 0.531 9.874 14449 Z= 0.305 Chirality : 0.039 0.230 1704 Planarity : 0.004 0.033 1319 Dihedral : 20.759 147.701 2949 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.47 % Allowed : 21.36 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.16 (0.29), residues: 817 helix: 1.71 (0.30), residues: 313 sheet: -0.82 (0.45), residues: 97 loop : -0.94 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.010 0.001 TYR A 960 PHE 0.011 0.002 PHE A 41 TRP 0.006 0.001 TRP A 16 HIS 0.003 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (10220) covalent geometry : angle 0.53076 / 0.30 (14449) hydrogen bonds : bond 0.05253 / 3.81 ( 418) hydrogen bonds : angle 3.96940 / 2.78 ( 1057) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.286 Fit side-chains REVERT: A 115 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8106 (ttp80) REVERT: A 140 LYS cc_start: 0.7103 (tttp) cc_final: 0.5212 (ptpp) REVERT: A 347 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.7493 (m) REVERT: A 350 LYS cc_start: 0.2771 (OUTLIER) cc_final: 0.0847 (pmtt) REVERT: A 395 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7076 (mp) REVERT: A 720 GLU cc_start: 0.5775 (OUTLIER) cc_final: 0.5147 (mt-10) REVERT: A 917 LYS cc_start: 0.8517 (mttp) cc_final: 0.8195 (mmtp) REVERT: A 1060 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8107 (tpp) REVERT: A 1065 ARG cc_start: 0.6849 (mpt180) cc_final: 0.6007 (mtm180) outliers start: 25 outliers final: 18 residues processed: 109 average time/residue: 0.6645 time to fit residues: 76.6421 Evaluate side-chains 112 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1016 ILE Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1091 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 0.0060 chunk 23 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 GLN A 389 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.156554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118324 restraints weight = 9206.667| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.29 r_work: 0.3208 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10220 Z= 0.113 Angle : 0.489 9.858 14449 Z= 0.286 Chirality : 0.037 0.226 1704 Planarity : 0.004 0.031 1319 Dihedral : 20.732 147.953 2949 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.61 % Allowed : 21.36 % Favored : 75.03 % 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: 0.33 (0.29), residues: 817 helix: 1.89 (0.30), residues: 313 sheet: -0.78 (0.46), residues: 97 loop : -0.86 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.009 0.001 TYR A 960 PHE 0.010 0.001 PHE A 41 TRP 0.006 0.001 TRP A 75 HIS 0.003 0.001 HIS A1100 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 (10220) covalent geometry : angle 0.48942 / 0.29 (14449) hydrogen bonds : bond 0.04663 / 3.38 ( 418) hydrogen bonds : angle 3.89549 / 2.73 ( 1057) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.204 Fit side-chains REVERT: A 115 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8086 (ttp80) REVERT: A 140 LYS cc_start: 0.7100 (tttp) cc_final: 0.5218 (ptpp) REVERT: A 345 LYS cc_start: 0.7881 (mtmm) cc_final: 0.7447 (ttpp) REVERT: A 347 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7467 (m) REVERT: A 350 LYS cc_start: 0.2771 (OUTLIER) cc_final: 0.0862 (pmtt) REVERT: A 528 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8122 (t) REVERT: A 720 GLU cc_start: 0.5778 (OUTLIER) cc_final: 0.5128 (mt-10) REVERT: A 877 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8168 (mtt-85) REVERT: A 917 LYS cc_start: 0.8501 (mttp) cc_final: 0.8179 (mmtp) REVERT: A 1065 ARG cc_start: 0.6811 (mpt180) cc_final: 0.5984 (mtm180) outliers start: 26 outliers final: 17 residues processed: 109 average time/residue: 0.6327 time to fit residues: 72.8649 Evaluate side-chains 109 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 ARG Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1091 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.153212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.114540 restraints weight = 9257.907| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.29 r_work: 0.3157 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10220 Z= 0.188 Angle : 0.569 10.027 14449 Z= 0.320 Chirality : 0.042 0.229 1704 Planarity : 0.005 0.034 1319 Dihedral : 20.710 148.058 2949 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.19 % Allowed : 22.05 % Favored : 74.76 % 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: 0.20 (0.28), residues: 817 helix: 1.79 (0.30), residues: 306 sheet: -0.75 (0.46), residues: 97 loop : -0.93 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 32 TYR 0.012 0.002 TYR A 960 PHE 0.014 0.002 PHE A1013 TRP 0.006 0.001 TRP A 16 HIS 0.004 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (10220) covalent geometry : angle 0.56908 / 0.32 (14449) hydrogen bonds : bond 0.05722 / 4.14 ( 418) hydrogen bonds : angle 3.99255 / 2.80 ( 1057) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3160.12 seconds wall clock time: 54 minutes 24.10 seconds (3264.10 seconds total)