Starting phenix.real_space_refine on Thu Jul 2 09:20:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izq_61039/07_2026/9izq_61039.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izq_61039/07_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_61039/07_2026/9izq_61039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izq_61039/07_2026/9izq_61039.map" model { file = "/net/cci-nas-00/data/ceres_data/9izq_61039/07_2026/9izq_61039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izq_61039/07_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): 0.01s 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: 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: 2.07, per 1000 atoms: 0.25 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: 0.93 Conformation dependent library (CDL) restraints added in 236.1 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: 1.39 Time building geometry restraints manager: 1.17 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: 11499 1.55 - 3.09: 377 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 - 0.034: 887 0.034 - 0.069: 329 0.069 - 0.103: 103 0.103 - 0.138: 27 0.138 - 0.172: 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 2.46 2.29 0.17 2.00e-01 2.50e+01 7.41e-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 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 2.46 2.30 0.15 2.00e-01 2.50e+01 5.98e-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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.050 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.750 ------------------------------------------------------------------------------- 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= 0.352 Angle : 0.608 7.733 11896 Z= 0.463 Chirality : 0.041 0.172 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 0.00488 / 0.35 ( 8512) covalent geometry : angle 0.60751 / 0.46 (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 : 0.267 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: 0.7503 (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: 0.1043 time to fit residues: 17.2194 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 : 0.249 ------------------------------------------------------------------------------- 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: 20.0000 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 599 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.175695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.126384 restraints weight = 10707.873| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.06 r_work: 0.3144 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8512 Z= 0.189 Angle : 0.568 7.235 11896 Z= 0.331 Chirality : 0.040 0.158 1350 Planarity : 0.003 0.031 1166 Dihedral : 20.745 101.831 2101 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.16 % Allowed : 11.90 % 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: -0.41 (0.31), residues: 737 helix: 0.47 (0.27), residues: 360 sheet: -0.33 (0.53), residues: 95 loop : -1.12 (0.38), residues: 282 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 0.028 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 0.00402 / 0.19 ( 8512) covalent geometry : angle 0.56762 / 0.33 (11896) hydrogen bonds : bond 0.05756 / 3.71 ( 357) hydrogen bonds : angle 4.45396 / 3.20 ( 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 93 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9019 (ttt) cc_final: 0.8655 (ttm) REVERT: A 356 ASP cc_start: 0.7936 (t0) cc_final: 0.7567 (t0) REVERT: A 452 LYS cc_start: 0.8437 (ttmm) cc_final: 0.7949 (ttmm) outliers start: 8 outliers final: 5 residues processed: 89 average time/residue: 0.0840 time to fit residues: 10.5097 Evaluate side-chains 76 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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: 0.9990 chunk 28 optimal weight: 6.9990 chunk 46 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 47 optimal weight: 30.0000 chunk 42 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.177628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128077 restraints weight = 10488.661| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.02 r_work: 0.3209 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8512 Z= 0.158 Angle : 0.515 8.499 11896 Z= 0.300 Chirality : 0.038 0.145 1350 Planarity : 0.003 0.027 1166 Dihedral : 20.701 101.324 2099 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.74 % Allowed : 11.90 % Favored : 86.36 % 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: -0.24 (0.31), residues: 737 helix: 0.72 (0.28), residues: 370 sheet: -0.29 (0.52), residues: 95 loop : -1.26 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 197 TYR 0.013 0.002 TYR A 93 PHE 0.025 0.002 PHE A 480 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 0.00330 / 0.16 ( 8512) covalent geometry : angle 0.51473 / 0.30 (11896) hydrogen bonds : bond 0.05097 / 3.26 ( 357) hydrogen bonds : angle 4.13313 / 2.96 ( 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 87 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9020 (ttt) cc_final: 0.8636 (ttm) REVERT: A 356 ASP cc_start: 0.7985 (t0) cc_final: 0.7636 (t0) REVERT: A 452 LYS cc_start: 0.8401 (ttmm) cc_final: 0.7873 (ttmm) REVERT: A 595 MET cc_start: 0.8037 (tpp) cc_final: 0.7767 (tpp) outliers start: 12 outliers final: 7 residues processed: 82 average time/residue: 0.0822 time to fit residues: 9.5086 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 : 0.246 ------------------------------------------------------------------------------- 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: 7.9990 chunk 58 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.175471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125632 restraints weight = 10792.429| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.03 r_work: 0.3161 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 8512 Z= 0.270 Angle : 0.604 9.128 11896 Z= 0.340 Chirality : 0.042 0.175 1350 Planarity : 0.003 0.026 1166 Dihedral : 20.755 101.924 2099 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.89 % Allowed : 14.22 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.31), residues: 737 helix: 0.58 (0.27), residues: 370 sheet: -0.56 (0.51), residues: 95 loop : -1.27 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 280 TYR 0.017 0.002 TYR A 93 PHE 0.034 0.003 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 0.00611 / 0.27 ( 8512) covalent geometry : angle 0.60375 / 0.34 (11896) hydrogen bonds : bond 0.05530 / 3.59 ( 357) hydrogen bonds : angle 4.13166 / 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 86 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8959 (ttt) cc_final: 0.8694 (ttm) REVERT: A 356 ASP cc_start: 0.7999 (t0) cc_final: 0.7688 (t0) outliers start: 13 outliers final: 10 residues processed: 80 average time/residue: 0.0803 time to fit residues: 8.9445 Evaluate side-chains 78 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 2 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.178365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129633 restraints weight = 10651.462| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.04 r_work: 0.3203 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8512 Z= 0.136 Angle : 0.493 8.748 11896 Z= 0.289 Chirality : 0.037 0.154 1350 Planarity : 0.003 0.025 1166 Dihedral : 20.674 100.741 2099 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.16 % Allowed : 15.97 % Favored : 82.87 % 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: -0.07 (0.31), residues: 737 helix: 0.94 (0.28), residues: 367 sheet: -0.38 (0.53), residues: 88 loop : -1.21 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 197 TYR 0.012 0.001 TYR A 437 PHE 0.025 0.002 PHE A 480 TRP 0.008 0.001 TRP A 696 HIS 0.002 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 ( 8512) covalent geometry : angle 0.49280 / 0.29 (11896) hydrogen bonds : bond 0.04538 / 2.89 ( 357) hydrogen bonds : angle 3.90666 / 2.79 ( 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 82 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9000 (ttt) cc_final: 0.8770 (ttm) REVERT: A 155 MET cc_start: 0.8281 (tpp) cc_final: 0.8039 (tpt) REVERT: A 356 ASP cc_start: 0.8044 (t0) cc_final: 0.7749 (t0) REVERT: A 588 LYS cc_start: 0.9098 (mmtt) cc_final: 0.8875 (mppt) REVERT: A 595 MET cc_start: 0.8098 (tpp) cc_final: 0.7844 (tpp) REVERT: A 667 ARG cc_start: 0.7985 (tpp80) cc_final: 0.7497 (tpp80) outliers start: 8 outliers final: 6 residues processed: 78 average time/residue: 0.0808 time to fit residues: 8.6673 Evaluate side-chains 73 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 711 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 72 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 ** 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 = 0.4099 r_free = 0.4099 target = 0.176563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126977 restraints weight = 10562.711| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.04 r_work: 0.3169 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 8512 Z= 0.219 Angle : 0.539 9.634 11896 Z= 0.310 Chirality : 0.040 0.158 1350 Planarity : 0.003 0.027 1166 Dihedral : 20.679 101.134 2099 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.03 % Allowed : 14.95 % 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: -0.19 (0.31), residues: 737 helix: 0.83 (0.27), residues: 368 sheet: -0.51 (0.51), residues: 95 loop : -1.23 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.015 0.002 TYR A 93 PHE 0.024 0.002 PHE A 612 TRP 0.010 0.002 TRP A 696 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 ( 8512) covalent geometry : angle 0.53936 / 0.31 (11896) hydrogen bonds : bond 0.05027 / 3.24 ( 357) hydrogen bonds : angle 3.90174 / 2.79 ( 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 85 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8919 (ttt) cc_final: 0.8636 (ttm) REVERT: A 356 ASP cc_start: 0.8093 (t0) cc_final: 0.7813 (t0) REVERT: A 458 MET cc_start: 0.8197 (tpt) cc_final: 0.7955 (tpp) REVERT: A 588 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8851 (mppt) REVERT: A 667 ARG cc_start: 0.8038 (tpp80) cc_final: 0.7555 (tpp80) outliers start: 14 outliers final: 10 residues processed: 80 average time/residue: 0.0762 time to fit residues: 8.4930 Evaluate side-chains 77 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 35 LYS 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 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: 3.9990 chunk 60 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 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 = 0.4096 r_free = 0.4096 target = 0.176682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.127100 restraints weight = 10623.551| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.01 r_work: 0.3167 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 8512 Z= 0.227 Angle : 0.553 9.430 11896 Z= 0.314 Chirality : 0.040 0.166 1350 Planarity : 0.003 0.023 1166 Dihedral : 20.666 101.200 2099 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: -0.23 (0.31), residues: 737 helix: 0.85 (0.27), residues: 367 sheet: -0.56 (0.53), residues: 88 loop : -1.30 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.016 0.002 TYR A 93 PHE 0.030 0.002 PHE A 480 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 0.00506 / 0.23 ( 8512) covalent geometry : angle 0.55254 / 0.31 (11896) hydrogen bonds : bond 0.04996 / 3.22 ( 357) hydrogen bonds : angle 3.88999 / 2.78 ( 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: 12 poor density : 68 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8926 (ttt) cc_final: 0.8645 (ttm) REVERT: A 155 MET cc_start: 0.8269 (tpp) cc_final: 0.8068 (tpt) REVERT: A 356 ASP cc_start: 0.8088 (t0) cc_final: 0.7803 (t0) REVERT: A 458 MET cc_start: 0.8255 (tpt) cc_final: 0.8016 (tpp) REVERT: A 588 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8841 (mppt) REVERT: A 706 LYS cc_start: 0.7824 (ptmm) cc_final: 0.7469 (ptmm) outliers start: 12 outliers final: 10 residues processed: 75 average time/residue: 0.0676 time to fit residues: 7.1618 Evaluate side-chains 76 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.176978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127633 restraints weight = 10552.029| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.00 r_work: 0.3186 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8512 Z= 0.186 Angle : 0.528 9.127 11896 Z= 0.302 Chirality : 0.039 0.155 1350 Planarity : 0.003 0.027 1166 Dihedral : 20.637 101.135 2099 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.60 % Allowed : 16.26 % Favored : 82.15 % 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: -0.01 (0.31), residues: 737 helix: 1.05 (0.28), residues: 361 sheet: -0.49 (0.53), residues: 88 loop : -1.17 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 667 TYR 0.014 0.002 TYR A 93 PHE 0.021 0.002 PHE A 612 TRP 0.009 0.001 TRP A 696 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 ( 8512) covalent geometry : angle 0.52765 / 0.30 (11896) hydrogen bonds : bond 0.04701 / 3.02 ( 357) hydrogen bonds : angle 3.82120 / 2.73 ( 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 80 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8912 (ttt) cc_final: 0.8648 (ttm) REVERT: A 356 ASP cc_start: 0.8093 (t0) cc_final: 0.7818 (t0) REVERT: A 458 MET cc_start: 0.8250 (tpt) cc_final: 0.8017 (tpp) REVERT: A 588 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8854 (mppt) REVERT: A 706 LYS cc_start: 0.7817 (ptmm) cc_final: 0.7455 (ptmm) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.0774 time to fit residues: 8.0998 Evaluate side-chains 75 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL 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 711 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 4 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.178916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130204 restraints weight = 10624.313| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.99 r_work: 0.3221 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8512 Z= 0.134 Angle : 0.510 8.921 11896 Z= 0.291 Chirality : 0.038 0.158 1350 Planarity : 0.003 0.026 1166 Dihedral : 20.582 99.763 2099 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.31 % Allowed : 16.26 % 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: 0.20 (0.31), residues: 737 helix: 1.22 (0.28), residues: 360 sheet: -0.33 (0.54), residues: 88 loop : -1.08 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 197 TYR 0.011 0.001 TYR A 23 PHE 0.024 0.002 PHE A 480 TRP 0.008 0.001 TRP A 268 HIS 0.002 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 8512) covalent geometry : angle 0.50968 / 0.29 (11896) hydrogen bonds : bond 0.04261 / 2.73 ( 357) hydrogen bonds : angle 3.73055 / 2.66 ( 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: 9 poor density : 73 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8774 (t) REVERT: A 63 MET cc_start: 0.8955 (ttt) cc_final: 0.8702 (ttm) REVERT: A 155 MET cc_start: 0.8044 (tpp) cc_final: 0.7834 (tpp) REVERT: A 356 ASP cc_start: 0.8056 (t0) cc_final: 0.7777 (t0) REVERT: A 458 MET cc_start: 0.8289 (tpt) cc_final: 0.8068 (tpp) REVERT: A 588 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8803 (mppt) REVERT: A 637 PHE cc_start: 0.7025 (m-80) cc_final: 0.6750 (m-80) REVERT: A 706 LYS cc_start: 0.7813 (ptmm) cc_final: 0.7454 (ptmm) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.0696 time to fit residues: 7.7240 Evaluate side-chains 77 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL 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 711 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.178743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129956 restraints weight = 10670.454| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.98 r_work: 0.3218 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8512 Z= 0.147 Angle : 0.527 8.929 11896 Z= 0.300 Chirality : 0.038 0.253 1350 Planarity : 0.003 0.034 1166 Dihedral : 20.557 99.281 2099 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.02 % Allowed : 16.40 % Favored : 82.58 % 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: 0.21 (0.31), residues: 737 helix: 1.22 (0.28), residues: 360 sheet: -0.32 (0.54), residues: 88 loop : -1.07 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 667 TYR 0.017 0.002 TYR A 94 PHE 0.024 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 0.00315 / 0.15 ( 8512) covalent geometry : angle 0.52663 / 0.30 (11896) hydrogen bonds : bond 0.04267 / 2.74 ( 357) hydrogen bonds : angle 3.73942 / 2.66 ( 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 77 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8768 (t) REVERT: A 63 MET cc_start: 0.8961 (ttt) cc_final: 0.8712 (ttm) REVERT: A 356 ASP cc_start: 0.8052 (t0) cc_final: 0.7783 (t0) REVERT: A 458 MET cc_start: 0.8288 (tpt) cc_final: 0.8074 (tpp) REVERT: A 588 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8801 (mppt) REVERT: A 637 PHE cc_start: 0.7085 (m-80) cc_final: 0.6827 (m-80) REVERT: A 667 ARG cc_start: 0.7840 (tpp80) cc_final: 0.7438 (tpp80) outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.0825 time to fit residues: 8.5921 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 : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL 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: 0.0070 chunk 14 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 80 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 overall best weight: 1.0402 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.180499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.132362 restraints weight = 10646.828| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.99 r_work: 0.3240 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8512 Z= 0.120 Angle : 0.503 9.099 11896 Z= 0.288 Chirality : 0.037 0.155 1350 Planarity : 0.003 0.044 1166 Dihedral : 20.513 98.325 2099 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.02 % Allowed : 16.55 % 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: 0.35 (0.31), residues: 737 helix: 1.40 (0.28), residues: 361 sheet: -0.23 (0.54), residues: 88 loop : -1.11 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 667 TYR 0.015 0.001 TYR A 94 PHE 0.022 0.002 PHE A 480 TRP 0.007 0.001 TRP A 33 HIS 0.003 0.000 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 ( 8512) covalent geometry : angle 0.50292 / 0.29 (11896) hydrogen bonds : bond 0.04004 / 2.56 ( 357) hydrogen bonds : angle 3.65737 / 2.60 ( 970) =============================================================================== Job complete usr+sys time: 1714.26 seconds wall clock time: 30 minutes 8.00 seconds (1808.00 seconds total)