Starting phenix.real_space_refine on Wed Aug 5 01:49:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izq_61039/08_2026/9izq_61039.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izq_61039/08_2026/9izq_61039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9izq_61039/08_2026/9izq_61039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izq_61039/08_2026/9izq_61039.map" model { file = "/net/cci-nas-00/data/ceres_data/9izq_61039/08_2026/9izq_61039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izq_61039/08_2026/9izq_61039.cif" } resolution = 3.06 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 ------------------------------------------------------------------------------- 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= 0.016 sd= 0.197 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 96 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 4864 2.51 5 N 1370 2.21 5 O 1799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s 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: 8161 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 6140 Classifications: {'peptide': 739} Link IDs: {'PTRANS': 12, 'TRANS': 726} Chain: "B" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1127 Classifications: {'RNA': 53} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 7, 'rna3p_pur': 24, 'rna3p_pyr': 19} Link IDs: {'rna2p': 9, 'rna3p': 43} Chain: "C" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 564 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.84, per 1000 atoms: 0.23 Number of scatterers: 8161 At special positions: 0 Unit cell: (90.885, 95.865, 109.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 96 15.00 Mg 2 11.99 O 1799 8.00 N 1370 7.00 C 4864 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: 0.78 Conformation dependent library (CDL) restraints added in 163.3 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 5 sheets defined 51.7% alpha, 9.2% beta 32 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 16 through 37 Processing helix chain 'A' and resid 42 through 54 removed outlier: 3.601A pdb=" N MET A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 85 through 99 removed outlier: 3.540A pdb=" N LYS A 98 " --> pdb=" O TYR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 119 through 134 Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.714A pdb=" N TRP A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 203 removed outlier: 4.039A pdb=" N GLU A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 218 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.512A pdb=" N ASN A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 287 removed outlier: 4.182A pdb=" N ASP A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 353 removed outlier: 3.657A pdb=" N LEU A 353 " --> pdb=" O TYR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.968A pdb=" N LEU A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.603A pdb=" N LYS A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 397 through 418 removed outlier: 3.756A pdb=" N GLN A 402 " --> pdb=" O CYS A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 459 removed outlier: 3.955A pdb=" N VAL A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 483 through 519 removed outlier: 3.618A pdb=" N LEU A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 519 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 571 removed outlier: 3.623A pdb=" N ASN A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 605 Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 614 through 623 removed outlier: 3.720A pdb=" N GLU A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 693 removed outlier: 3.513A pdb=" N TYR A 689 " --> pdb=" O ASN A 685 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 701 removed outlier: 3.587A pdb=" N GLU A 698 " --> pdb=" O GLU A 694 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 237 removed outlier: 6.892A pdb=" N ASN A 290 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER A 305 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 300 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 5 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU A 266 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 242 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 376 through 379 removed outlier: 5.345A pdb=" N GLU A 336 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N PHE A 379 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR A 334 " --> pdb=" O PHE A 379 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY A 322 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N LYS A 337 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 12.887A pdb=" N THR A 320 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 321 " --> pdb=" O ALA A 524 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N GLU A 526 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N LEU A 323 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 578 removed outlier: 3.764A pdb=" N ASP A 586 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 650 through 652 Processing sheet with id=AA5, first strand: chain 'A' and resid 667 through 668 removed outlier: 3.679A pdb=" N LYS A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 1.03 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: 1695 1.33 - 1.45: 2338 1.45 - 1.57: 4242 1.57 - 1.69: 190 1.69 - 1.81: 47 Bond restraints: 8512 Sorted by residual: bond pdb=" C3' DC D 19 " pdb=" C2' DC D 19 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DT C -4 " pdb=" C2' DT C -4 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.62e+00 bond pdb=" C3' DT C -2 " pdb=" O3' DT C -2 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.22e+00 bond pdb=" C3' DG D 27 " pdb=" C2' DG D 27 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.72e+00 bond pdb=" C3' DT C -3 " pdb=" O3' DT C -3 " ideal model delta sigma weight residual 1.435 1.402 0.033 1.30e-02 5.92e+03 6.41e+00 ... (remaining 8507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 11362 1.55 - 3.09: 514 3.09 - 4.64: 18 4.64 - 6.19: 1 6.19 - 7.73: 1 Bond angle restraints: 11896 Sorted by residual: angle pdb=" O4' DC D 20 " pdb=" C4' DC D 20 " pdb=" C3' DC D 20 " ideal model delta sigma weight residual 106.00 103.31 2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT D 13 " pdb=" C4 DT D 13 " pdb=" O4 DT D 13 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT D 25 " pdb=" C4 DT D 25 " pdb=" O4 DT D 25 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT C 5 " pdb=" C4 DT C 5 " pdb=" O4 DT C 5 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT C -3 " pdb=" C4 DT C -3 " pdb=" O4 DT C -3 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 ... (remaining 11891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.05: 4432 20.05 - 40.10: 452 40.10 - 60.15: 210 60.15 - 80.20: 38 80.20 - 100.25: 2 Dihedral angle restraints: 5134 sinusoidal: 2924 harmonic: 2210 Sorted by residual: dihedral pdb=" CA ARG A 420 " pdb=" C ARG A 420 " pdb=" N THR A 421 " pdb=" CA THR A 421 " ideal model delta harmonic sigma weight residual 180.00 -162.52 -17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASP A 67 " pdb=" CB ASP A 67 " pdb=" CG ASP A 67 " pdb=" OD1 ASP A 67 " ideal model delta sinusoidal sigma weight residual -30.00 -88.12 58.12 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CB GLU A 692 " pdb=" CG GLU A 692 " pdb=" CD GLU A 692 " pdb=" OE1 GLU A 692 " ideal model delta sinusoidal sigma weight residual 0.00 -89.70 89.70 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 877 0.037 - 0.074: 312 0.074 - 0.111: 101 0.111 - 0.148: 56 0.148 - 0.185: 4 Chirality restraints: 1350 Sorted by residual: chirality pdb=" C1' G B 1 " pdb=" O4' G B 1 " pdb=" C2' G B 1 " pdb=" N9 G B 1 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" C1' G B -33 " pdb=" O4' G B -33 " pdb=" C2' G B -33 " pdb=" N9 G B -33 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" C3' DC D 12 " pdb=" C4' DC D 12 " pdb=" O3' DC D 12 " pdb=" C2' DC D 12 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 1347 not shown) Planarity restraints: 1166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 1 " -0.028 2.00e-02 2.50e+03 1.20e-02 4.35e+00 pdb=" N9 G B 1 " 0.029 2.00e-02 2.50e+03 pdb=" C8 G B 1 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G B 1 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B 1 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B 1 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G B 1 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G B 1 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 1 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 1 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 1 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G B 1 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B -33 " -0.025 2.00e-02 2.50e+03 1.09e-02 3.55e+00 pdb=" N9 G B -33 " 0.027 2.00e-02 2.50e+03 pdb=" C8 G B -33 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G B -33 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B -33 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B -33 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G B -33 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G B -33 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G B -33 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B -33 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B -33 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G B -33 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 633 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A 634 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 634 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 634 " -0.020 5.00e-02 4.00e+02 ... (remaining 1163 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 99 2.62 - 3.19: 6720 3.19 - 3.76: 13225 3.76 - 4.33: 19401 4.33 - 4.90: 28690 Nonbonded interactions: 68135 Sorted by model distance: nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A 801 " model vdw 2.052 2.170 nonbonded pdb=" OP1 G B -30 " pdb="MG MG A 801 " model vdw 2.111 2.170 nonbonded pdb=" OH TYR A 512 " pdb=" O THR A 628 " model vdw 2.149 3.040 nonbonded pdb=" OD1 ASP A 462 " pdb=" O2' C B 14 " model vdw 2.167 3.040 nonbonded pdb=" ND2 ASN A 532 " pdb=" OG SER A 635 " model vdw 2.172 3.120 ... (remaining 68130 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.160 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 0.035 8512 Z= 0.358 Angle : 0.665 7.733 11896 Z= 0.510 Chirality : 0.048 0.185 1350 Planarity : 0.003 0.036 1166 Dihedral : 18.612 100.252 3706 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.58 % Allowed : 7.40 % Favored : 92.02 % 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: -0.74 (0.31), residues: 737 helix: 0.14 (0.27), residues: 363 sheet: -0.32 (0.58), residues: 84 loop : -1.26 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 697 TYR 0.014 0.002 TYR A 437 PHE 0.011 0.002 PHE A 612 TRP 0.008 0.001 TRP A 696 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.36 ( 8512) covalent geometry : angle 0.66496 / 0.51 (11896) hydrogen bonds : bond 0.18919 / 12.22 ( 357) hydrogen bonds : angle 6.11187 / 4.38 ( 970) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9059 (ttt) cc_final: 0.8719 (ttm) REVERT: A 356 ASP cc_start: 0.7909 (t0) cc_final: 0.7504 (t0) REVERT: A 589 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.6539 (m-80) outliers start: 4 outliers final: 0 residues processed: 128 average time/residue: 0.1072 time to fit residues: 17.7230 Evaluate side-chains 81 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 297 ASN A 506 ASN A 517 GLN A 530 ASN A 537 GLN A 599 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.175725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126332 restraints weight = 10716.492| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.04 r_work: 0.3144 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8512 Z= 0.188 Angle : 0.571 7.181 11896 Z= 0.332 Chirality : 0.040 0.148 1350 Planarity : 0.003 0.031 1166 Dihedral : 20.683 100.296 2101 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.02 % Allowed : 12.05 % Favored : 86.94 % 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: -0.43 (0.31), residues: 737 helix: 0.46 (0.27), residues: 362 sheet: -0.35 (0.54), residues: 94 loop : -1.15 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 133 TYR 0.014 0.002 TYR A 93 PHE 0.030 0.002 PHE A 612 TRP 0.010 0.002 TRP A 696 HIS 0.003 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 ( 8512) covalent geometry : angle 0.57148 / 0.33 (11896) hydrogen bonds : bond 0.05928 / 3.82 ( 357) hydrogen bonds : angle 4.47359 / 3.22 ( 970) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9027 (ttt) cc_final: 0.8664 (ttm) REVERT: A 88 ASP cc_start: 0.8092 (m-30) cc_final: 0.7884 (m-30) REVERT: A 356 ASP cc_start: 0.7939 (t0) cc_final: 0.7572 (t0) REVERT: A 452 LYS cc_start: 0.8497 (ttmm) cc_final: 0.8020 (ttmm) outliers start: 7 outliers final: 5 residues processed: 88 average time/residue: 0.0726 time to fit residues: 9.0200 Evaluate side-chains 73 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 40.0000 chunk 42 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.176457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.126679 restraints weight = 10484.924| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.98 r_work: 0.3164 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 8512 Z= 0.229 Angle : 0.578 9.107 11896 Z= 0.326 Chirality : 0.041 0.147 1350 Planarity : 0.003 0.026 1166 Dihedral : 20.682 99.890 2099 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.03 % Allowed : 11.76 % Favored : 86.21 % 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: -0.43 (0.31), residues: 737 helix: 0.56 (0.27), residues: 370 sheet: -0.42 (0.51), residues: 95 loop : -1.33 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.014 0.002 TYR A 93 PHE 0.027 0.002 PHE A 612 TRP 0.012 0.002 TRP A 696 HIS 0.002 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.23 ( 8512) covalent geometry : angle 0.57786 / 0.33 (11896) hydrogen bonds : bond 0.05588 / 3.61 ( 357) hydrogen bonds : angle 4.21696 / 3.02 ( 970) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9033 (ttt) cc_final: 0.8682 (ttm) REVERT: A 356 ASP cc_start: 0.8014 (t0) cc_final: 0.7671 (t0) REVERT: A 452 LYS cc_start: 0.8437 (ttmm) cc_final: 0.7902 (ttmm) REVERT: A 694 GLU cc_start: 0.8065 (mp0) cc_final: 0.7853 (mp0) outliers start: 14 outliers final: 7 residues processed: 84 average time/residue: 0.0785 time to fit residues: 9.2966 Evaluate side-chains 76 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** 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 = 0.4097 r_free = 0.4097 target = 0.176370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126504 restraints weight = 10744.078| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.97 r_work: 0.3154 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 8512 Z= 0.243 Angle : 0.590 9.234 11896 Z= 0.331 Chirality : 0.042 0.148 1350 Planarity : 0.003 0.025 1166 Dihedral : 20.688 99.841 2099 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.60 % Allowed : 14.66 % Favored : 83.74 % 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: -0.49 (0.31), residues: 737 helix: 0.54 (0.27), residues: 370 sheet: -0.61 (0.51), residues: 95 loop : -1.33 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 697 TYR 0.016 0.002 TYR A 93 PHE 0.033 0.002 PHE A 612 TRP 0.010 0.002 TRP A 696 HIS 0.002 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.24 ( 8512) covalent geometry : angle 0.58974 / 0.33 (11896) hydrogen bonds : bond 0.05367 / 3.46 ( 357) hydrogen bonds : angle 4.12214 / 2.96 ( 970) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8963 (ttt) cc_final: 0.8712 (ttm) REVERT: A 356 ASP cc_start: 0.8023 (t0) cc_final: 0.7715 (t0) REVERT: A 667 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7659 (tpp80) outliers start: 11 outliers final: 11 residues processed: 81 average time/residue: 0.0884 time to fit residues: 9.8325 Evaluate side-chains 77 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 725 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 23 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 13 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.178836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.129653 restraints weight = 10626.752| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.99 r_work: 0.3197 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8512 Z= 0.150 Angle : 0.513 9.313 11896 Z= 0.295 Chirality : 0.038 0.142 1350 Planarity : 0.003 0.025 1166 Dihedral : 20.629 98.780 2099 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.45 % Allowed : 16.11 % Favored : 82.44 % 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: -0.23 (0.31), residues: 737 helix: 0.88 (0.28), residues: 367 sheet: -0.70 (0.54), residues: 86 loop : -1.29 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 667 TYR 0.011 0.002 TYR A 93 PHE 0.025 0.002 PHE A 612 TRP 0.009 0.001 TRP A 696 HIS 0.002 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 8512) covalent geometry : angle 0.51325 / 0.30 (11896) hydrogen bonds : bond 0.04702 / 3.01 ( 357) hydrogen bonds : angle 3.93252 / 2.81 ( 970) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8998 (ttt) cc_final: 0.8771 (ttm) REVERT: A 155 MET cc_start: 0.8281 (tpp) cc_final: 0.8043 (tpt) REVERT: A 356 ASP cc_start: 0.8072 (t0) cc_final: 0.7781 (t0) REVERT: A 458 MET cc_start: 0.8180 (tpt) cc_final: 0.7944 (tpp) REVERT: A 588 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8879 (mppt) REVERT: A 667 ARG cc_start: 0.8111 (tpp80) cc_final: 0.7540 (tpp80) outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 0.0746 time to fit residues: 7.9906 Evaluate side-chains 73 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 30.0000 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.178787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129903 restraints weight = 10580.551| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.03 r_work: 0.3209 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8512 Z= 0.138 Angle : 0.493 9.117 11896 Z= 0.285 Chirality : 0.038 0.142 1350 Planarity : 0.003 0.027 1166 Dihedral : 20.571 97.445 2099 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.74 % Allowed : 15.82 % Favored : 82.44 % 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 (0.32), residues: 737 helix: 1.15 (0.28), residues: 361 sheet: -0.38 (0.52), residues: 95 loop : -1.04 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 667 TYR 0.011 0.001 TYR A 23 PHE 0.028 0.002 PHE A 480 TRP 0.009 0.001 TRP A 696 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 8512) covalent geometry : angle 0.49349 / 0.29 (11896) hydrogen bonds : bond 0.04425 / 2.83 ( 357) hydrogen bonds : angle 3.78074 / 2.70 ( 970) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7485 (ppp) cc_final: 0.7099 (ttp) REVERT: A 63 MET cc_start: 0.8990 (ttt) cc_final: 0.8751 (ttm) REVERT: A 356 ASP cc_start: 0.8094 (t0) cc_final: 0.7811 (t0) REVERT: A 458 MET cc_start: 0.8243 (tpt) cc_final: 0.8006 (tpp) REVERT: A 588 LYS cc_start: 0.9071 (mmtt) cc_final: 0.8850 (mppt) REVERT: A 667 ARG cc_start: 0.7861 (tpp80) cc_final: 0.7304 (tpp80) REVERT: A 706 LYS cc_start: 0.7805 (ptmm) cc_final: 0.7570 (ptmm) outliers start: 12 outliers final: 8 residues processed: 82 average time/residue: 0.0726 time to fit residues: 8.1933 Evaluate side-chains 78 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 30.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN A 675 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.178587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129624 restraints weight = 10663.035| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.02 r_work: 0.3206 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8512 Z= 0.154 Angle : 0.513 8.931 11896 Z= 0.293 Chirality : 0.038 0.209 1350 Planarity : 0.003 0.025 1166 Dihedral : 20.551 96.865 2099 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.60 % Allowed : 15.67 % Favored : 82.73 % 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: 0.15 (0.31), residues: 737 helix: 1.15 (0.28), residues: 360 sheet: -0.37 (0.54), residues: 88 loop : -1.04 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 667 TYR 0.013 0.002 TYR A 93 PHE 0.020 0.002 PHE A 612 TRP 0.008 0.001 TRP A 696 HIS 0.001 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 8512) covalent geometry : angle 0.51328 / 0.29 (11896) hydrogen bonds : bond 0.04413 / 2.83 ( 357) hydrogen bonds : angle 3.77977 / 2.69 ( 970) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7566 (ppp) cc_final: 0.7045 (ttp) REVERT: A 63 MET cc_start: 0.8962 (ttt) cc_final: 0.8720 (ttm) REVERT: A 155 MET cc_start: 0.8198 (tpp) cc_final: 0.7965 (tpt) REVERT: A 356 ASP cc_start: 0.8074 (t0) cc_final: 0.7800 (t0) REVERT: A 458 MET cc_start: 0.8244 (tpt) cc_final: 0.8007 (tpp) REVERT: A 588 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8841 (mppt) REVERT: A 667 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7319 (tpp80) REVERT: A 706 LYS cc_start: 0.7810 (ptmm) cc_final: 0.7539 (ptmm) outliers start: 11 outliers final: 8 residues processed: 75 average time/residue: 0.0726 time to fit residues: 7.7428 Evaluate side-chains 76 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 77 optimal weight: 30.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.177830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128630 restraints weight = 10603.384| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.95 r_work: 0.3197 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8512 Z= 0.176 Angle : 0.525 8.818 11896 Z= 0.299 Chirality : 0.039 0.148 1350 Planarity : 0.003 0.026 1166 Dihedral : 20.534 96.490 2099 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.60 % Allowed : 15.38 % Favored : 83.02 % 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: 0.14 (0.31), residues: 737 helix: 1.16 (0.27), residues: 360 sheet: -0.41 (0.54), residues: 88 loop : -1.06 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 133 TYR 0.015 0.002 TYR A 93 PHE 0.028 0.002 PHE A 480 TRP 0.008 0.001 TRP A 696 HIS 0.002 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 ( 8512) covalent geometry : angle 0.52549 / 0.30 (11896) hydrogen bonds : bond 0.04550 / 2.93 ( 357) hydrogen bonds : angle 3.75221 / 2.68 ( 970) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7495 (ppp) cc_final: 0.7127 (ttp) REVERT: A 63 MET cc_start: 0.8904 (ttt) cc_final: 0.8632 (ttm) REVERT: A 356 ASP cc_start: 0.8042 (t0) cc_final: 0.7763 (t0) REVERT: A 458 MET cc_start: 0.8292 (tpt) cc_final: 0.8064 (tpp) REVERT: A 588 LYS cc_start: 0.9068 (mmtt) cc_final: 0.8797 (mppt) REVERT: A 637 PHE cc_start: 0.7020 (m-80) cc_final: 0.6736 (m-80) REVERT: A 667 ARG cc_start: 0.7908 (tpp80) cc_final: 0.7376 (tpp80) REVERT: A 706 LYS cc_start: 0.7806 (ptmm) cc_final: 0.7515 (ptmm) outliers start: 11 outliers final: 11 residues processed: 78 average time/residue: 0.0707 time to fit residues: 7.7936 Evaluate side-chains 79 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 4 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.177830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128771 restraints weight = 10668.207| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.97 r_work: 0.3194 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8512 Z= 0.175 Angle : 0.530 8.594 11896 Z= 0.299 Chirality : 0.039 0.155 1350 Planarity : 0.003 0.027 1166 Dihedral : 20.515 96.368 2099 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.74 % Allowed : 15.09 % Favored : 83.16 % 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: 0.12 (0.31), residues: 737 helix: 1.21 (0.27), residues: 361 sheet: -0.45 (0.54), residues: 85 loop : -1.16 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 280 TYR 0.015 0.002 TYR A 93 PHE 0.025 0.002 PHE A 480 TRP 0.008 0.001 TRP A 696 HIS 0.002 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 ( 8512) covalent geometry : angle 0.53027 / 0.30 (11896) hydrogen bonds : bond 0.04525 / 2.91 ( 357) hydrogen bonds : angle 3.75565 / 2.68 ( 970) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7587 (ppp) cc_final: 0.7175 (ttp) REVERT: A 63 MET cc_start: 0.8909 (ttt) cc_final: 0.8639 (ttm) REVERT: A 356 ASP cc_start: 0.8050 (t0) cc_final: 0.7766 (t0) REVERT: A 458 MET cc_start: 0.8291 (tpt) cc_final: 0.8066 (tpp) REVERT: A 588 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8799 (mppt) REVERT: A 667 ARG cc_start: 0.7903 (tpp80) cc_final: 0.7376 (tpp80) REVERT: A 706 LYS cc_start: 0.7761 (ptmm) cc_final: 0.7499 (ptmm) outliers start: 12 outliers final: 11 residues processed: 77 average time/residue: 0.0672 time to fit residues: 7.3005 Evaluate side-chains 80 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 69 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.179659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131029 restraints weight = 10687.146| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.96 r_work: 0.3231 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8512 Z= 0.123 Angle : 0.496 8.495 11896 Z= 0.284 Chirality : 0.037 0.159 1350 Planarity : 0.003 0.030 1166 Dihedral : 20.468 95.494 2099 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.02 % Allowed : 15.67 % Favored : 83.31 % 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: 0.35 (0.31), residues: 737 helix: 1.43 (0.28), residues: 361 sheet: -0.23 (0.57), residues: 78 loop : -1.13 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 390 TYR 0.012 0.001 TYR A 437 PHE 0.023 0.002 PHE A 480 TRP 0.008 0.001 TRP A 268 HIS 0.001 0.000 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 8512) covalent geometry : angle 0.49606 / 0.28 (11896) hydrogen bonds : bond 0.04077 / 2.62 ( 357) hydrogen bonds : angle 3.67418 / 2.61 ( 970) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7575 (ppp) cc_final: 0.7316 (ttp) REVERT: A 63 MET cc_start: 0.8949 (ttt) cc_final: 0.8698 (ttm) REVERT: A 458 MET cc_start: 0.8288 (tpt) cc_final: 0.8074 (tpp) REVERT: A 588 LYS cc_start: 0.9089 (mmtt) cc_final: 0.8796 (mppt) REVERT: A 637 PHE cc_start: 0.7014 (m-80) cc_final: 0.6764 (m-80) REVERT: A 667 ARG cc_start: 0.7909 (tpp80) cc_final: 0.7383 (tpp80) outliers start: 7 outliers final: 6 residues processed: 77 average time/residue: 0.0754 time to fit residues: 7.9000 Evaluate side-chains 76 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 27 optimal weight: 0.0370 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 46 optimal weight: 30.0000 chunk 63 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 30.0000 overall best weight: 2.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN ** A 555 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 = 0.4121 r_free = 0.4121 target = 0.178613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.129645 restraints weight = 10640.293| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.00 r_work: 0.3219 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8512 Z= 0.161 Angle : 0.517 8.383 11896 Z= 0.294 Chirality : 0.038 0.157 1350 Planarity : 0.003 0.031 1166 Dihedral : 20.458 95.405 2099 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.02 % Allowed : 15.82 % Favored : 83.16 % 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: 0.37 (0.31), residues: 737 helix: 1.43 (0.28), residues: 358 sheet: -0.37 (0.54), residues: 85 loop : -1.02 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 434 TYR 0.014 0.002 TYR A 93 PHE 0.023 0.002 PHE A 480 TRP 0.007 0.001 TRP A 696 HIS 0.004 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 8512) covalent geometry : angle 0.51726 / 0.29 (11896) hydrogen bonds : bond 0.04303 / 2.77 ( 357) hydrogen bonds : angle 3.68254 / 2.61 ( 970) =============================================================================== Job complete usr+sys time: 1593.77 seconds wall clock time: 28 minutes 0.43 seconds (1680.43 seconds total)