Starting phenix.real_space_refine on Thu Jul 2 14:14:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfs_61438/07_2026/9jfs_61438.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfs_61438/07_2026/9jfs_61438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jfs_61438/07_2026/9jfs_61438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfs_61438/07_2026/9jfs_61438.map" model { file = "/net/cci-nas-00/data/ceres_data/9jfs_61438/07_2026/9jfs_61438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfs_61438/07_2026/9jfs_61438.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 175 5.49 5 S 17 5.16 5 C 4904 2.51 5 N 1579 2.21 5 O 2121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8796 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4285 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 21, 'TRANS': 507} Chain breaks: 2 Chain: "B" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2938 Classifications: {'RNA': 138} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 64, 'rna3p_pyr': 60} Link IDs: {'rna2p': 14, 'rna3p': 123} Chain breaks: 3 Chain: "C" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 546 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 225 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Time building chain proxies: 1.76, per 1000 atoms: 0.20 Number of scatterers: 8796 At special positions: 0 Unit cell: (108.992, 101.504, 123.968, 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 17 16.00 P 175 15.00 O 2121 8.00 N 1579 7.00 C 4904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 567 " distance=2.04 Simple disulfide: pdb=" SG CYS E 33 " - pdb=" SG CYS E 36 " distance=2.03 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: 0.71 Conformation dependent library (CDL) restraints added in 199.0 milliseconds 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1198 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 5 sheets defined 52.2% alpha, 11.4% beta 68 base pairs and 107 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 11 through 64 removed outlier: 4.795A pdb=" N CYS A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL A 42 " --> pdb=" O HIS A 38 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 79 removed outlier: 3.779A pdb=" N GLN A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 96 removed outlier: 3.610A pdb=" N LEU A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 182 through 186 removed outlier: 3.975A pdb=" N PHE A 185 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 186 " --> pdb=" O GLY A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 182 through 186' Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 198 through 209 Processing helix chain 'A' and resid 217 through 237 removed outlier: 3.554A pdb=" N ILE A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 345 through 365 Processing helix chain 'A' and resid 396 through 428 removed outlier: 4.311A pdb=" N GLU A 400 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 472 Processing helix chain 'A' and resid 480 through 485 removed outlier: 4.284A pdb=" N ASN A 483 " --> pdb=" O THR A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 519 through 535 Processing helix chain 'A' and resid 581 through 593 Processing helix chain 'E' and resid 12 through 18 Processing helix chain 'E' and resid 33 through 50 removed outlier: 3.857A pdb=" N LYS E 37 " --> pdb=" O CYS E 33 " (cutoff:3.500A) Proline residue: E 41 - end of helix removed outlier: 3.621A pdb=" N ASP E 48 " --> pdb=" O ASP E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 71 removed outlier: 3.964A pdb=" N LYS E 70 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR E 71 " --> pdb=" O THR E 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 66 through 71' Processing helix chain 'E' and resid 96 through 108 Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 260 removed outlier: 6.603A pdb=" N ALA A 320 " --> pdb=" O PRO A 301 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR A 303 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR A 313 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A 284 " --> pdb=" O LYS A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128 Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 393 removed outlier: 3.914A pdb=" N VAL A 385 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 475 " --> pdb=" O HIS A 539 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 564 through 565 Processing sheet with id=AA5, first strand: chain 'E' and resid 6 through 7 removed outlier: 6.494A pdb=" N ILE E 6 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASN E 60 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU E 25 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU E 59 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASP E 27 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR E 78 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU E 79 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR E 90 " --> pdb=" O LEU E 79 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU E 81 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU E 86 " --> pdb=" O LYS E 83 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 170 hydrogen bonds 332 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 107 stacking parallelities Total time for adding SS restraints: 1.83 Time building geometry restraints manager: 0.96 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: 2142 1.33 - 1.46: 2831 1.46 - 1.58: 3998 1.58 - 1.70: 344 1.70 - 1.82: 22 Bond restraints: 9337 Sorted by residual: bond pdb=" C1' DT D 10 " pdb=" N1 DT D 10 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 9.90e+00 bond pdb=" N1 C B 177 " pdb=" C6 C B 177 " ideal model delta sigma weight residual 1.367 1.352 0.015 6.00e-03 2.78e+04 6.65e+00 bond pdb=" C4' DA C 12 " pdb=" C3' DA C 12 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.59e+00 bond pdb=" C1' DT C 24 " pdb=" N1 DT C 24 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.55e+00 bond pdb=" C4 C B 180 " pdb=" C5 C B 180 " ideal model delta sigma weight residual 1.425 1.405 0.020 8.00e-03 1.56e+04 6.37e+00 ... (remaining 9332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 12563 1.02 - 2.04: 686 2.04 - 3.06: 139 3.06 - 4.07: 46 4.07 - 5.09: 4 Bond angle restraints: 13438 Sorted by residual: angle pdb=" N3 DT C 18 " pdb=" C4 DT C 18 " pdb=" O4 DT C 18 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT D 6 " pdb=" C4 DT D 6 " pdb=" O4 DT D 6 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" N3 DT D 10 " pdb=" C4 DT D 10 " pdb=" O4 DT D 10 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.60e+01 angle pdb=" C1' C B 98 " pdb=" N1 C B 98 " pdb=" C2 C B 98 " ideal model delta sigma weight residual 118.80 123.12 -4.32 1.10e+00 8.26e-01 1.54e+01 angle pdb=" C1' G B 7 " pdb=" N9 G B 7 " pdb=" C4 G B 7 " ideal model delta sigma weight residual 126.50 131.59 -5.09 1.30e+00 5.92e-01 1.53e+01 ... (remaining 13433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.41: 5207 31.41 - 62.82: 425 62.82 - 94.23: 79 94.23 - 125.63: 1 125.63 - 157.04: 2 Dihedral angle restraints: 5714 sinusoidal: 3871 harmonic: 1843 Sorted by residual: dihedral pdb=" C4' A B 105 " pdb=" C3' A B 105 " pdb=" O3' A B 105 " pdb=" P U B 106 " ideal model delta sinusoidal sigma weight residual -110.00 47.04 -157.04 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' U B 181 " pdb=" C3' U B 181 " pdb=" O3' U B 181 " pdb=" P U B 182 " ideal model delta sinusoidal sigma weight residual 220.00 75.72 144.28 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" O4' U B 174 " pdb=" C1' U B 174 " pdb=" N1 U B 174 " pdb=" C2 U B 174 " ideal model delta sinusoidal sigma weight residual -128.00 -74.00 -54.00 1 1.70e+01 3.46e-03 1.37e+01 ... (remaining 5711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1269 0.043 - 0.086: 248 0.086 - 0.129: 63 0.129 - 0.173: 28 0.173 - 0.216: 5 Chirality restraints: 1613 Sorted by residual: chirality pdb=" C3' DA C 15 " pdb=" C4' DA C 15 " pdb=" O3' DA C 15 " pdb=" C2' DA C 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C3' DC C 20 " pdb=" C4' DC C 20 " pdb=" O3' DC C 20 " pdb=" C2' DC C 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C1' G B 175 " pdb=" O4' G B 175 " pdb=" C2' G B 175 " pdb=" N9 G B 175 " both_signs ideal model delta sigma weight residual False 2.46 2.28 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1610 not shown) Planarity restraints: 1071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 178 " -0.032 2.00e-02 2.50e+03 1.59e-02 5.71e+00 pdb=" N1 C B 178 " 0.032 2.00e-02 2.50e+03 pdb=" C2 C B 178 " 0.003 2.00e-02 2.50e+03 pdb=" O2 C B 178 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C B 178 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C B 178 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C B 178 " -0.011 2.00e-02 2.50e+03 pdb=" C5 C B 178 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C B 178 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 175 " -0.029 2.00e-02 2.50e+03 1.29e-02 4.98e+00 pdb=" N9 G B 175 " 0.032 2.00e-02 2.50e+03 pdb=" C8 G B 175 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G B 175 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B 175 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 175 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G B 175 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G B 175 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 175 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 175 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G B 175 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 175 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 8 " -0.027 2.00e-02 2.50e+03 1.48e-02 4.95e+00 pdb=" N1 U B 8 " 0.034 2.00e-02 2.50e+03 pdb=" C2 U B 8 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U B 8 " 0.006 2.00e-02 2.50e+03 pdb=" N3 U B 8 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U B 8 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U B 8 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U B 8 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U B 8 " 0.002 2.00e-02 2.50e+03 ... (remaining 1068 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 35 2.55 - 3.14: 6494 3.14 - 3.72: 14522 3.72 - 4.31: 21297 4.31 - 4.90: 30731 Nonbonded interactions: 73079 Sorted by model distance: nonbonded pdb=" OD2 ASP A 414 " pdb=" O2' U B 185 " model vdw 1.960 3.040 nonbonded pdb=" O2' U B 181 " pdb=" O5' U B 182 " model vdw 2.129 3.040 nonbonded pdb=" OE1 GLU A 417 " pdb=" NH2 ARG A 433 " model vdw 2.180 3.120 nonbonded pdb=" N ASP E 10 " pdb=" OD1 ASN E 64 " model vdw 2.209 3.120 nonbonded pdb=" O GLY A 201 " pdb=" OG1 THR A 204 " model vdw 2.212 3.040 ... (remaining 73074 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: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.740 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 0.044 9339 Z= 0.435 Angle : 0.569 5.092 13442 Z= 0.476 Chirality : 0.043 0.216 1613 Planarity : 0.004 0.032 1071 Dihedral : 19.720 157.041 4510 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.53 % Allowed : 2.84 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.49 (0.34), residues: 626 helix: 2.55 (0.31), residues: 300 sheet: 0.32 (0.55), residues: 73 loop : -0.77 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 293 TYR 0.007 0.001 TYR A 314 PHE 0.013 0.002 PHE E 82 TRP 0.011 0.002 TRP A 47 HIS 0.004 0.001 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.43 ( 9337) covalent geometry : angle 0.56850 / 0.48 (13438) SS BOND : bond 0.00388 / 0.20 ( 2) SS BOND : angle 0.83418 / 0.43 ( 4) hydrogen bonds : bond 0.10661 / 6.75 ( 436) hydrogen bonds : angle 4.15313 / 3.00 ( 1085) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.230 Fit side-chains REVERT: A 359 GLU cc_start: 0.7606 (tp30) cc_final: 0.7284 (tp30) REVERT: A 372 ASP cc_start: 0.7612 (t0) cc_final: 0.7208 (t0) REVERT: A 382 GLN cc_start: 0.7601 (tt0) cc_final: 0.7390 (tt0) REVERT: E 8 LEU cc_start: 0.5697 (mp) cc_final: 0.5481 (mp) outliers start: 3 outliers final: 1 residues processed: 99 average time/residue: 0.6561 time to fit residues: 68.3924 Evaluate side-chains 96 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 GLN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN A 569 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.143897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113620 restraints weight = 12943.139| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.46 r_work: 0.3337 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 9339 Z= 0.327 Angle : 0.599 6.289 13442 Z= 0.346 Chirality : 0.047 0.259 1613 Planarity : 0.005 0.037 1071 Dihedral : 22.209 166.833 3210 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.24 % Allowed : 7.98 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.41 (0.33), residues: 626 helix: 2.34 (0.30), residues: 303 sheet: 0.37 (0.57), residues: 72 loop : -0.68 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 206 TYR 0.012 0.002 TYR A 314 PHE 0.019 0.003 PHE E 82 TRP 0.022 0.003 TRP A 424 HIS 0.008 0.002 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.33 ( 9337) covalent geometry : angle 0.59905 / 0.35 (13438) SS BOND : bond 0.00352 / 0.19 ( 2) SS BOND : angle 1.16016 / 0.57 ( 4) hydrogen bonds : bond 0.07813 / 5.23 ( 436) hydrogen bonds : angle 3.57836 / 2.61 ( 1085) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.208 Fit side-chains REVERT: A 359 GLU cc_start: 0.7767 (tp30) cc_final: 0.7464 (tp30) REVERT: A 372 ASP cc_start: 0.7610 (t0) cc_final: 0.7236 (t0) REVERT: A 382 GLN cc_start: 0.7784 (tt0) cc_final: 0.7541 (tt0) REVERT: A 421 ASP cc_start: 0.7891 (m-30) cc_final: 0.7629 (m-30) REVERT: A 478 GLU cc_start: 0.6768 (tp30) cc_final: 0.6553 (tp30) REVERT: E 8 LEU cc_start: 0.6032 (mp) cc_final: 0.5776 (mp) outliers start: 7 outliers final: 3 residues processed: 101 average time/residue: 0.6639 time to fit residues: 70.7638 Evaluate side-chains 101 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain E residue 33 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 32 optimal weight: 0.0270 chunk 75 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.146329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116215 restraints weight = 12981.894| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.43 r_work: 0.3377 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9339 Z= 0.157 Angle : 0.479 5.752 13442 Z= 0.289 Chirality : 0.038 0.227 1613 Planarity : 0.004 0.037 1071 Dihedral : 22.242 166.226 3210 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.95 % Allowed : 9.93 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.78 (0.33), residues: 626 helix: 2.69 (0.30), residues: 303 sheet: 0.46 (0.57), residues: 72 loop : -0.52 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 206 TYR 0.014 0.001 TYR A 45 PHE 0.015 0.002 PHE E 82 TRP 0.017 0.002 TRP A 47 HIS 0.004 0.001 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 ( 9337) covalent geometry : angle 0.47903 / 0.29 (13438) SS BOND : bond 0.00300 / 0.15 ( 2) SS BOND : angle 0.81740 / 0.41 ( 4) hydrogen bonds : bond 0.06048 / 4.05 ( 436) hydrogen bonds : angle 3.32011 / 2.42 ( 1085) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.218 Fit side-chains REVERT: A 269 ASP cc_start: 0.8229 (t0) cc_final: 0.8002 (t70) REVERT: A 359 GLU cc_start: 0.7772 (tp30) cc_final: 0.7430 (tp30) REVERT: A 372 ASP cc_start: 0.7628 (t0) cc_final: 0.7259 (t0) REVERT: A 382 GLN cc_start: 0.7752 (tt0) cc_final: 0.7498 (tt0) REVERT: A 421 ASP cc_start: 0.7905 (m-30) cc_final: 0.7634 (m-30) REVERT: E 8 LEU cc_start: 0.5890 (mp) cc_final: 0.5643 (mp) outliers start: 11 outliers final: 5 residues processed: 103 average time/residue: 0.6155 time to fit residues: 66.9206 Evaluate side-chains 100 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 33 CYS Chi-restraints excluded: chain E residue 46 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.146108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115978 restraints weight = 13083.347| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.44 r_work: 0.3371 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9339 Z= 0.175 Angle : 0.480 5.641 13442 Z= 0.287 Chirality : 0.038 0.237 1613 Planarity : 0.004 0.038 1071 Dihedral : 22.238 167.214 3210 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.13 % Allowed : 10.46 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.84 (0.34), residues: 626 helix: 2.80 (0.30), residues: 303 sheet: 0.50 (0.58), residues: 72 loop : -0.58 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 433 TYR 0.021 0.002 TYR A 45 PHE 0.013 0.002 PHE A 228 TRP 0.015 0.002 TRP A 424 HIS 0.005 0.001 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 ( 9337) covalent geometry : angle 0.48024 / 0.29 (13438) SS BOND : bond 0.00281 / 0.14 ( 2) SS BOND : angle 0.79233 / 0.39 ( 4) hydrogen bonds : bond 0.05999 / 4.01 ( 436) hydrogen bonds : angle 3.23602 / 2.36 ( 1085) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.181 Fit side-chains REVERT: A 269 ASP cc_start: 0.8238 (t0) cc_final: 0.8016 (t70) REVERT: A 359 GLU cc_start: 0.7783 (tp30) cc_final: 0.7458 (tp30) REVERT: A 372 ASP cc_start: 0.7628 (t0) cc_final: 0.7266 (t0) REVERT: A 382 GLN cc_start: 0.7783 (tt0) cc_final: 0.7536 (tt0) REVERT: A 414 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: E 8 LEU cc_start: 0.5954 (mp) cc_final: 0.5707 (mp) outliers start: 12 outliers final: 6 residues processed: 103 average time/residue: 0.5719 time to fit residues: 62.2928 Evaluate side-chains 102 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain E residue 33 CYS Chi-restraints excluded: chain E residue 46 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.0470 chunk 44 optimal weight: 0.5980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.147059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117117 restraints weight = 13011.909| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.43 r_work: 0.3388 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9339 Z= 0.143 Angle : 0.450 5.769 13442 Z= 0.273 Chirality : 0.037 0.229 1613 Planarity : 0.004 0.037 1071 Dihedral : 22.253 166.382 3210 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.95 % Allowed : 10.64 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.34), residues: 626 helix: 2.98 (0.30), residues: 303 sheet: 0.60 (0.59), residues: 72 loop : -0.50 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 433 TYR 0.018 0.001 TYR A 45 PHE 0.012 0.002 PHE E 82 TRP 0.014 0.002 TRP A 47 HIS 0.004 0.001 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 9337) covalent geometry : angle 0.44961 / 0.27 (13438) SS BOND : bond 0.00267 / 0.13 ( 2) SS BOND : angle 0.75882 / 0.39 ( 4) hydrogen bonds : bond 0.05448 / 3.65 ( 436) hydrogen bonds : angle 3.14502 / 2.29 ( 1085) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.203 Fit side-chains REVERT: A 269 ASP cc_start: 0.8196 (t0) cc_final: 0.7971 (t70) REVERT: A 359 GLU cc_start: 0.7798 (tp30) cc_final: 0.7494 (tp30) REVERT: A 372 ASP cc_start: 0.7633 (t0) cc_final: 0.7294 (t0) REVERT: A 382 GLN cc_start: 0.7786 (tt0) cc_final: 0.7534 (tt0) REVERT: A 414 ASP cc_start: 0.8140 (m-30) cc_final: 0.7803 (m-30) REVERT: A 417 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7291 (mm-30) REVERT: E 8 LEU cc_start: 0.5866 (mp) cc_final: 0.5648 (mp) outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.5336 time to fit residues: 58.6999 Evaluate side-chains 102 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain E residue 33 CYS Chi-restraints excluded: chain E residue 46 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 51 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115734 restraints weight = 13068.104| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.44 r_work: 0.3370 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9339 Z= 0.194 Angle : 0.481 5.606 13442 Z= 0.287 Chirality : 0.039 0.244 1613 Planarity : 0.004 0.037 1071 Dihedral : 22.245 168.290 3210 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.84 % Allowed : 10.82 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.95 (0.34), residues: 626 helix: 2.92 (0.30), residues: 303 sheet: 0.49 (0.59), residues: 72 loop : -0.55 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 206 TYR 0.017 0.001 TYR A 45 PHE 0.013 0.002 PHE A 228 TRP 0.016 0.002 TRP A 424 HIS 0.005 0.001 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 ( 9337) covalent geometry : angle 0.48131 / 0.29 (13438) SS BOND : bond 0.00257 / 0.13 ( 2) SS BOND : angle 0.80058 / 0.40 ( 4) hydrogen bonds : bond 0.06028 / 4.03 ( 436) hydrogen bonds : angle 3.17491 / 2.30 ( 1085) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.200 Fit side-chains REVERT: A 269 ASP cc_start: 0.8231 (t0) cc_final: 0.8004 (t70) REVERT: A 359 GLU cc_start: 0.7810 (tp30) cc_final: 0.7504 (tp30) REVERT: A 372 ASP cc_start: 0.7638 (t0) cc_final: 0.7298 (t0) REVERT: A 382 GLN cc_start: 0.7814 (tt0) cc_final: 0.7544 (tt0) REVERT: A 414 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7799 (m-30) REVERT: A 417 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7443 (mm-30) outliers start: 16 outliers final: 8 residues processed: 105 average time/residue: 0.5067 time to fit residues: 56.3524 Evaluate side-chains 101 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain E residue 33 CYS Chi-restraints excluded: chain E residue 46 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.142869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112782 restraints weight = 13023.702| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.49 r_work: 0.3330 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 9339 Z= 0.377 Angle : 0.616 7.300 13442 Z= 0.356 Chirality : 0.050 0.297 1613 Planarity : 0.005 0.044 1071 Dihedral : 22.340 172.661 3210 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.30 % Allowed : 11.88 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.36 (0.33), residues: 626 helix: 2.41 (0.29), residues: 303 sheet: 0.10 (0.56), residues: 73 loop : -0.77 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 206 TYR 0.021 0.002 TYR A 45 PHE 0.017 0.003 PHE A 235 TRP 0.026 0.003 TRP A 424 HIS 0.007 0.002 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00792 / 0.38 ( 9337) covalent geometry : angle 0.61608 / 0.36 (13438) SS BOND : bond 0.00252 / 0.13 ( 2) SS BOND : angle 0.85055 / 0.41 ( 4) hydrogen bonds : bond 0.08191 / 5.55 ( 436) hydrogen bonds : angle 3.45734 / 2.52 ( 1085) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 269 ASP cc_start: 0.8268 (t0) cc_final: 0.8024 (t70) REVERT: A 359 GLU cc_start: 0.7771 (tp30) cc_final: 0.7450 (tp30) REVERT: A 372 ASP cc_start: 0.7645 (t0) cc_final: 0.7296 (t0) REVERT: A 382 GLN cc_start: 0.7822 (tt0) cc_final: 0.7560 (tt0) REVERT: A 407 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7559 (mm-30) REVERT: A 414 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: A 417 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7424 (mm-30) REVERT: A 478 GLU cc_start: 0.6758 (tp30) cc_final: 0.6469 (tp30) outliers start: 13 outliers final: 8 residues processed: 101 average time/residue: 0.6633 time to fit residues: 70.8834 Evaluate side-chains 104 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain E residue 33 CYS Chi-restraints excluded: chain E residue 46 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.145357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115387 restraints weight = 13032.575| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.44 r_work: 0.3364 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9339 Z= 0.176 Angle : 0.492 6.220 13442 Z= 0.294 Chirality : 0.039 0.244 1613 Planarity : 0.004 0.038 1071 Dihedral : 22.351 167.853 3210 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.30 % Allowed : 12.59 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.73 (0.34), residues: 626 helix: 2.75 (0.30), residues: 303 sheet: 0.23 (0.57), residues: 73 loop : -0.62 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 433 TYR 0.019 0.001 TYR A 45 PHE 0.014 0.002 PHE E 82 TRP 0.020 0.002 TRP A 424 HIS 0.004 0.001 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 ( 9337) covalent geometry : angle 0.49238 / 0.29 (13438) SS BOND : bond 0.00273 / 0.14 ( 2) SS BOND : angle 0.76006 / 0.39 ( 4) hydrogen bonds : bond 0.06097 / 4.11 ( 436) hydrogen bonds : angle 3.24283 / 2.36 ( 1085) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.193 Fit side-chains REVERT: A 269 ASP cc_start: 0.8267 (t0) cc_final: 0.8038 (t70) REVERT: A 359 GLU cc_start: 0.7810 (tp30) cc_final: 0.7493 (tp30) REVERT: A 372 ASP cc_start: 0.7632 (t0) cc_final: 0.7283 (t0) REVERT: A 382 GLN cc_start: 0.7815 (tt0) cc_final: 0.7559 (tt0) REVERT: A 414 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: A 417 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7428 (mm-30) outliers start: 13 outliers final: 6 residues processed: 102 average time/residue: 0.5775 time to fit residues: 62.4220 Evaluate side-chains 99 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain E residue 33 CYS Chi-restraints excluded: chain E residue 46 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 36 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.0870 chunk 65 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115816 restraints weight = 12955.513| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.43 r_work: 0.3372 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9339 Z= 0.172 Angle : 0.482 5.841 13442 Z= 0.287 Chirality : 0.038 0.239 1613 Planarity : 0.004 0.038 1071 Dihedral : 22.316 167.491 3210 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.95 % Allowed : 12.77 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.88 (0.34), residues: 626 helix: 2.85 (0.30), residues: 303 sheet: 0.33 (0.57), residues: 72 loop : -0.53 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 433 TYR 0.011 0.001 TYR A 304 PHE 0.014 0.002 PHE E 82 TRP 0.020 0.002 TRP A 424 HIS 0.004 0.001 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 ( 9337) covalent geometry : angle 0.48219 / 0.29 (13438) SS BOND : bond 0.00262 / 0.13 ( 2) SS BOND : angle 0.75088 / 0.38 ( 4) hydrogen bonds : bond 0.05877 / 3.94 ( 436) hydrogen bonds : angle 3.19292 / 2.31 ( 1085) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.240 Fit side-chains REVERT: A 269 ASP cc_start: 0.8251 (t0) cc_final: 0.8036 (t70) REVERT: A 359 GLU cc_start: 0.7822 (tp30) cc_final: 0.7505 (tp30) REVERT: A 372 ASP cc_start: 0.7638 (t0) cc_final: 0.7293 (t0) REVERT: A 382 GLN cc_start: 0.7812 (tt0) cc_final: 0.7541 (tt0) REVERT: A 414 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7753 (m-30) outliers start: 11 outliers final: 7 residues processed: 101 average time/residue: 0.5796 time to fit residues: 62.1052 Evaluate side-chains 101 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 33 CYS Chi-restraints excluded: chain E residue 46 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0570 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.0070 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.117641 restraints weight = 13037.403| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.43 r_work: 0.3400 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9339 Z= 0.126 Angle : 0.452 6.020 13442 Z= 0.272 Chirality : 0.036 0.221 1613 Planarity : 0.004 0.038 1071 Dihedral : 22.314 165.921 3210 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.60 % Allowed : 13.65 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.34), residues: 626 helix: 3.00 (0.30), residues: 303 sheet: 0.40 (0.55), residues: 79 loop : -0.49 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 433 TYR 0.010 0.001 TYR A 314 PHE 0.013 0.002 PHE E 82 TRP 0.019 0.002 TRP A 47 HIS 0.003 0.001 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 ( 9337) covalent geometry : angle 0.45160 / 0.27 (13438) SS BOND : bond 0.00282 / 0.14 ( 2) SS BOND : angle 0.75408 / 0.39 ( 4) hydrogen bonds : bond 0.05159 / 3.46 ( 436) hydrogen bonds : angle 3.09765 / 2.24 ( 1085) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.147 Fit side-chains REVERT: A 186 GLU cc_start: 0.8095 (tt0) cc_final: 0.7873 (tt0) REVERT: A 269 ASP cc_start: 0.8240 (t0) cc_final: 0.8034 (t70) REVERT: A 359 GLU cc_start: 0.7821 (tp30) cc_final: 0.7523 (tp30) REVERT: A 382 GLN cc_start: 0.7793 (tt0) cc_final: 0.7529 (tt0) REVERT: A 414 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7700 (m-30) outliers start: 9 outliers final: 6 residues processed: 99 average time/residue: 0.6120 time to fit residues: 64.1036 Evaluate side-chains 98 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain E residue 33 CYS Chi-restraints excluded: chain E residue 46 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.0970 chunk 49 optimal weight: 0.0030 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.117613 restraints weight = 12908.871| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.43 r_work: 0.3398 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9339 Z= 0.130 Angle : 0.449 5.945 13442 Z= 0.269 Chirality : 0.036 0.225 1613 Planarity : 0.004 0.037 1071 Dihedral : 22.288 166.576 3210 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.60 % Allowed : 13.48 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.34), residues: 626 helix: 3.04 (0.30), residues: 303 sheet: 0.45 (0.55), residues: 78 loop : -0.41 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 433 TYR 0.011 0.001 TYR A 314 PHE 0.012 0.001 PHE E 82 TRP 0.018 0.002 TRP A 47 HIS 0.003 0.001 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 9337) covalent geometry : angle 0.44872 / 0.27 (13438) SS BOND : bond 0.00263 / 0.13 ( 2) SS BOND : angle 0.73892 / 0.38 ( 4) hydrogen bonds : bond 0.05158 / 3.44 ( 436) hydrogen bonds : angle 3.05754 / 2.20 ( 1085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3276.89 seconds wall clock time: 56 minutes 28.65 seconds (3388.65 seconds total)