Starting phenix.real_space_refine on Thu Jul 2 06:35:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nhb_49407/07_2026/9nhb_49407.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nhb_49407/07_2026/9nhb_49407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nhb_49407/07_2026/9nhb_49407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nhb_49407/07_2026/9nhb_49407.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nhb_49407/07_2026/9nhb_49407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nhb_49407/07_2026/9nhb_49407.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.071 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 46 5.49 5 Mg 1 5.21 5 S 28 5.16 5 C 4311 2.51 5 N 1232 2.21 5 O 1439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 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: 7057 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6040 Classifications: {'peptide': 748} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 713} Chain breaks: 3 Chain: "B" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 498 Classifications: {'RNA': 23} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 14, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 20} Chain: "C" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 479 Classifications: {'RNA': 23} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 12} Link IDs: {'rna2p': 2, 'rna3p': 20} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "A" 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: 1.78, per 1000 atoms: 0.25 Number of scatterers: 7057 At special positions: 0 Unit cell: (73.71, 88.27, 107.38, 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 28 16.00 P 46 15.00 Mg 1 11.99 O 1439 8.00 N 1232 7.00 C 4311 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: 0.65 Conformation dependent library (CDL) restraints added in 393.1 milliseconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1426 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 12 sheets defined 33.8% alpha, 20.1% beta 14 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 246 through 262 removed outlier: 3.869A pdb=" N ASN A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 330 removed outlier: 3.520A pdb=" N MET A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 342 removed outlier: 3.518A pdb=" N VAL A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.523A pdb=" N ASP A 443 " --> pdb=" O MET A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 467 removed outlier: 3.651A pdb=" N PHE A 464 " --> pdb=" O PHE A 460 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 477 removed outlier: 3.534A pdb=" N TRP A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 558 removed outlier: 3.722A pdb=" N LEU A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 591 removed outlier: 3.545A pdb=" N TYR A 579 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 580 " --> pdb=" O PRO A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 4.048A pdb=" N TYR A 607 " --> pdb=" O TYR A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 630 Processing helix chain 'A' and resid 634 through 650 Processing helix chain 'A' and resid 710 through 729 removed outlier: 3.917A pdb=" N GLY A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.857A pdb=" N SER A 752 " --> pdb=" O PRO A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 767 Processing helix chain 'A' and resid 842 through 853 Processing helix chain 'A' and resid 867 through 883 Processing helix chain 'A' and resid 889 through 893 removed outlier: 4.010A pdb=" N ASN A 893 " --> pdb=" O TYR A 890 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 150 removed outlier: 6.866A pdb=" N PHE A 775 " --> pdb=" O ILE A 835 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP A 837 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 773 " --> pdb=" O ASP A 837 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE A 735 " --> pdb=" O ALA A 774 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ILE A 776 " --> pdb=" O ILE A 735 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE A 737 " --> pdb=" O ILE A 776 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 778 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG A 739 " --> pdb=" O VAL A 778 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N MET A 665 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TYR A 738 " --> pdb=" O MET A 665 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL A 667 " --> pdb=" O TYR A 738 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 488 removed outlier: 3.572A pdb=" N SER A 793 " --> pdb=" O ARG A 790 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 157 through 159 removed outlier: 3.724A pdb=" N ASN A 296 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 271 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 157 through 159 removed outlier: 3.724A pdb=" N ASN A 296 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 285 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 205 through 208 Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=AA7, first strand: chain 'A' and resid 369 through 371 Processing sheet with id=AA8, first strand: chain 'A' and resid 399 through 401 Processing sheet with id=AA9, first strand: chain 'A' and resid 497 through 500 removed outlier: 3.730A pdb=" N TYR A 506 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 569 through 571 removed outlier: 6.356A pdb=" N VAL A 535 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE A 571 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR A 537 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 534 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL A 598 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE A 536 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 595 " --> pdb=" O GLN A 623 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL A 625 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS A 597 " --> pdb=" O VAL A 625 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 672 through 673 Processing sheet with id=AB3, first strand: chain 'A' and resid 687 through 688 248 hydrogen bonds defined for protein. 684 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 0.81 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: 1598 1.33 - 1.45: 1733 1.45 - 1.57: 3828 1.57 - 1.69: 90 1.69 - 1.82: 45 Bond restraints: 7294 Sorted by residual: bond pdb=" C4 C C 17 " pdb=" N4 C C 17 " ideal model delta sigma weight residual 1.335 1.297 0.038 9.00e-03 1.23e+04 1.77e+01 bond pdb=" C4 C C 10 " pdb=" N4 C C 10 " ideal model delta sigma weight residual 1.335 1.298 0.037 9.00e-03 1.23e+04 1.72e+01 bond pdb=" C4 C C 19 " pdb=" N4 C C 19 " ideal model delta sigma weight residual 1.335 1.298 0.037 9.00e-03 1.23e+04 1.69e+01 bond pdb=" C4 C B 11 " pdb=" N4 C B 11 " ideal model delta sigma weight residual 1.335 1.298 0.037 9.00e-03 1.23e+04 1.66e+01 bond pdb=" C2 G B 7 " pdb=" N2 G B 7 " ideal model delta sigma weight residual 1.341 1.300 0.041 1.00e-02 1.00e+04 1.64e+01 ... (remaining 7289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 9727 3.61 - 7.22: 343 7.22 - 10.83: 13 10.83 - 14.44: 3 14.44 - 18.05: 2 Bond angle restraints: 10088 Sorted by residual: angle pdb=" C3' G B 22 " pdb=" O3' G B 22 " pdb=" P A B 23 " ideal model delta sigma weight residual 120.20 102.15 18.05 1.50e+00 4.44e-01 1.45e+02 angle pdb=" N6 A C 12 " pdb=" C6 A C 12 " pdb=" N1 A C 12 " ideal model delta sigma weight residual 118.60 112.72 5.88 6.00e-01 2.78e+00 9.60e+01 angle pdb=" C3' U B 21 " pdb=" O3' U B 21 " pdb=" P G B 22 " ideal model delta sigma weight residual 120.20 106.68 13.52 1.50e+00 4.44e-01 8.13e+01 angle pdb=" C3' U B 20 " pdb=" O3' U B 20 " pdb=" P U B 21 " ideal model delta sigma weight residual 120.20 107.11 13.09 1.50e+00 4.44e-01 7.62e+01 angle pdb=" N6 A B 12 " pdb=" C6 A B 12 " pdb=" N1 A B 12 " ideal model delta sigma weight residual 118.60 113.39 5.21 6.00e-01 2.78e+00 7.55e+01 ... (remaining 10083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.02: 4070 23.02 - 46.04: 298 46.04 - 69.06: 91 69.06 - 92.07: 16 92.07 - 115.09: 2 Dihedral angle restraints: 4477 sinusoidal: 2264 harmonic: 2213 Sorted by residual: dihedral pdb=" O4' U C 3 " pdb=" C2' U C 3 " pdb=" C1' U C 3 " pdb=" C3' U C 3 " ideal model delta sinusoidal sigma weight residual 25.00 -16.74 41.74 1 8.00e+00 1.56e-02 3.81e+01 dihedral pdb=" C4' U C 3 " pdb=" O4' U C 3 " pdb=" C1' U C 3 " pdb=" C2' U C 3 " ideal model delta sinusoidal sigma weight residual 3.00 -36.09 39.09 1 8.00e+00 1.56e-02 3.36e+01 dihedral pdb=" CA THR A 537 " pdb=" C THR A 537 " pdb=" N PRO A 538 " pdb=" CA PRO A 538 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 4474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1005 0.118 - 0.236: 135 0.236 - 0.354: 22 0.354 - 0.472: 7 0.472 - 0.590: 3 Chirality restraints: 1172 Sorted by residual: chirality pdb=" P A C 25 " pdb=" OP1 A C 25 " pdb=" OP2 A C 25 " pdb=" O5' A C 25 " both_signs ideal model delta sigma weight residual True 2.41 -3.00 -0.59 2.00e-01 2.50e+01 8.70e+00 chirality pdb=" P U C 3 " pdb=" OP1 U C 3 " pdb=" OP2 U C 3 " pdb=" O5' U C 3 " both_signs ideal model delta sigma weight residual True 2.41 2.93 -0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" P U B 1 " pdb=" OP1 U B 1 " pdb=" OP2 U B 1 " pdb=" O5' U B 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.86e+00 ... (remaining 1169 not shown) Planarity restraints: 1113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 7 " -0.108 2.00e-02 2.50e+03 7.38e-02 1.63e+02 pdb=" N9 G B 7 " -0.017 2.00e-02 2.50e+03 pdb=" C8 G B 7 " 0.145 2.00e-02 2.50e+03 pdb=" N7 G B 7 " 0.082 2.00e-02 2.50e+03 pdb=" C5 G B 7 " -0.029 2.00e-02 2.50e+03 pdb=" C6 G B 7 " -0.055 2.00e-02 2.50e+03 pdb=" O6 G B 7 " -0.065 2.00e-02 2.50e+03 pdb=" N1 G B 7 " -0.013 2.00e-02 2.50e+03 pdb=" C2 G B 7 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G B 7 " 0.124 2.00e-02 2.50e+03 pdb=" N3 G B 7 " -0.026 2.00e-02 2.50e+03 pdb=" C4 G B 7 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 16 " -0.093 2.00e-02 2.50e+03 5.85e-02 1.03e+02 pdb=" N9 G B 16 " 0.006 2.00e-02 2.50e+03 pdb=" C8 G B 16 " 0.094 2.00e-02 2.50e+03 pdb=" N7 G B 16 " 0.068 2.00e-02 2.50e+03 pdb=" C5 G B 16 " -0.006 2.00e-02 2.50e+03 pdb=" C6 G B 16 " -0.040 2.00e-02 2.50e+03 pdb=" O6 G B 16 " -0.056 2.00e-02 2.50e+03 pdb=" N1 G B 16 " -0.021 2.00e-02 2.50e+03 pdb=" C2 G B 16 " -0.020 2.00e-02 2.50e+03 pdb=" N2 G B 16 " 0.111 2.00e-02 2.50e+03 pdb=" N3 G B 16 " -0.025 2.00e-02 2.50e+03 pdb=" C4 G B 16 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 749 " -0.092 2.00e-02 2.50e+03 5.02e-02 5.04e+01 pdb=" CG TYR A 749 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 749 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR A 749 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR A 749 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR A 749 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 749 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 749 " -0.074 2.00e-02 2.50e+03 ... (remaining 1110 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 25 2.51 - 3.11: 4793 3.11 - 3.71: 10772 3.71 - 4.30: 15050 4.30 - 4.90: 24953 Nonbonded interactions: 55593 Sorted by model distance: nonbonded pdb=" OD2 ASP A 670 " pdb="MG MG A 901 " model vdw 1.913 2.170 nonbonded pdb=" OD1 ASP A 670 " pdb="MG MG A 901 " model vdw 1.939 2.170 nonbonded pdb=" OD2 ASP A 740 " pdb="MG MG A 901 " model vdw 2.006 2.170 nonbonded pdb=" OP1 U C 16 " pdb="MG MG A 901 " model vdw 2.031 2.170 nonbonded pdb=" OD2 ASP A 690 " pdb=" OG1 THR A 694 " model vdw 2.177 3.040 ... (remaining 55588 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.130 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.010 0.059 7294 Z= 0.638 Angle : 1.537 18.046 10088 Z= 1.101 Chirality : 0.092 0.590 1172 Planarity : 0.013 0.164 1113 Dihedral : 17.435 115.092 3051 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.30 % Allowed : 11.14 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.29), residues: 742 helix: -0.79 (0.33), residues: 226 sheet: -1.22 (0.39), residues: 170 loop : -1.66 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 269 TYR 0.092 0.011 TYR A 749 PHE 0.043 0.006 PHE A 878 TRP 0.088 0.018 TRP A 166 HIS 0.009 0.002 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00977 / 0.64 ( 7294) covalent geometry : angle 1.53746 / 1.10 (10088) hydrogen bonds : bond 0.19025 / 12.86 ( 269) hydrogen bonds : angle 8.11175 / 5.57 ( 752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.250 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 113 average time/residue: 0.1116 time to fit residues: 16.0449 Evaluate side-chains 72 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 ASN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.162941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141031 restraints weight = 8957.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144106 restraints weight = 5479.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.146270 restraints weight = 3908.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147653 restraints weight = 3059.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.148726 restraints weight = 2574.567| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7294 Z= 0.147 Angle : 0.620 9.088 10088 Z= 0.337 Chirality : 0.044 0.206 1172 Planarity : 0.005 0.041 1113 Dihedral : 17.052 105.730 1537 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.08 % Allowed : 14.26 % Favored : 83.66 % 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: -1.06 (0.30), residues: 742 helix: 0.52 (0.34), residues: 228 sheet: -0.99 (0.37), residues: 185 loop : -1.33 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 781 TYR 0.015 0.002 TYR A 350 PHE 0.010 0.002 PHE A 775 TRP 0.012 0.002 TRP A 166 HIS 0.005 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 7294) covalent geometry : angle 0.61956 / 0.34 (10088) hydrogen bonds : bond 0.05802 / 3.99 ( 269) hydrogen bonds : angle 5.86080 / 3.93 ( 752) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.7371 (ttp) cc_final: 0.6826 (tmm) REVERT: A 779 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8318 (p) REVERT: A 799 PRO cc_start: 0.8578 (Cg_exo) cc_final: 0.8176 (Cg_endo) outliers start: 14 outliers final: 12 residues processed: 90 average time/residue: 0.1072 time to fit residues: 12.5858 Evaluate side-chains 86 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 838 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 376 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 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 = 0.3812 r_free = 0.3812 target = 0.156067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133967 restraints weight = 9063.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.136892 restraints weight = 5712.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138926 restraints weight = 4115.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.140330 restraints weight = 3252.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.141105 restraints weight = 2755.969| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 7294 Z= 0.200 Angle : 0.604 7.501 10088 Z= 0.327 Chirality : 0.044 0.144 1172 Planarity : 0.005 0.038 1113 Dihedral : 16.717 105.351 1537 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.86 % Allowed : 13.82 % Favored : 82.32 % 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: -1.10 (0.30), residues: 742 helix: 0.55 (0.34), residues: 234 sheet: -1.08 (0.38), residues: 181 loop : -1.40 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 739 TYR 0.019 0.002 TYR A 669 PHE 0.011 0.001 PHE A 370 TRP 0.013 0.002 TRP A 533 HIS 0.005 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 ( 7294) covalent geometry : angle 0.60411 / 0.33 (10088) hydrogen bonds : bond 0.05218 / 3.66 ( 269) hydrogen bonds : angle 5.55528 / 3.71 ( 752) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.261 Fit side-chains REVERT: A 189 MET cc_start: 0.7663 (ttp) cc_final: 0.7389 (tmm) REVERT: A 567 ASP cc_start: 0.6781 (t0) cc_final: 0.6519 (t0) REVERT: A 669 TYR cc_start: 0.7480 (m-10) cc_final: 0.6388 (m-80) REVERT: A 799 PRO cc_start: 0.8592 (Cg_exo) cc_final: 0.8256 (Cg_endo) outliers start: 26 outliers final: 17 residues processed: 103 average time/residue: 0.1038 time to fit residues: 14.0616 Evaluate side-chains 92 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 892 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.157310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135987 restraints weight = 9158.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.139268 restraints weight = 6130.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142318 restraints weight = 3953.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142470 restraints weight = 2981.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.142604 restraints weight = 2702.199| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7294 Z= 0.195 Angle : 0.588 8.605 10088 Z= 0.317 Chirality : 0.044 0.137 1172 Planarity : 0.004 0.039 1113 Dihedral : 16.604 102.017 1537 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.42 % Allowed : 15.45 % Favored : 81.13 % 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: -1.14 (0.30), residues: 742 helix: 0.58 (0.35), residues: 234 sheet: -1.02 (0.38), residues: 179 loop : -1.53 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 739 TYR 0.018 0.002 TYR A 669 PHE 0.009 0.001 PHE A 370 TRP 0.011 0.001 TRP A 533 HIS 0.004 0.001 HIS A 855 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 ( 7294) covalent geometry : angle 0.58837 / 0.32 (10088) hydrogen bonds : bond 0.04749 / 3.28 ( 269) hydrogen bonds : angle 5.43682 / 3.62 ( 752) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.259 Fit side-chains REVERT: A 799 PRO cc_start: 0.8558 (Cg_exo) cc_final: 0.8237 (Cg_endo) outliers start: 23 outliers final: 18 residues processed: 96 average time/residue: 0.1093 time to fit residues: 13.6617 Evaluate side-chains 91 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 860 CYS Chi-restraints excluded: chain A residue 892 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.157500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135970 restraints weight = 9083.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138786 restraints weight = 5861.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.140721 restraints weight = 4263.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142007 restraints weight = 3405.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.142890 restraints weight = 2899.383| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7294 Z= 0.177 Angle : 0.563 7.141 10088 Z= 0.303 Chirality : 0.043 0.156 1172 Planarity : 0.004 0.037 1113 Dihedral : 16.547 101.083 1537 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.71 % Allowed : 15.75 % Favored : 80.53 % 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: -1.03 (0.30), residues: 742 helix: 0.64 (0.34), residues: 235 sheet: -0.85 (0.39), residues: 173 loop : -1.52 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 562 TYR 0.034 0.002 TYR A 669 PHE 0.008 0.001 PHE A 370 TRP 0.009 0.001 TRP A 533 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 7294) covalent geometry : angle 0.56267 / 0.30 (10088) hydrogen bonds : bond 0.04395 / 3.04 ( 269) hydrogen bonds : angle 5.32254 / 3.54 ( 752) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.251 Fit side-chains REVERT: A 189 MET cc_start: 0.7574 (tmm) cc_final: 0.7050 (tmm) REVERT: A 567 ASP cc_start: 0.6668 (t0) cc_final: 0.6467 (t0) REVERT: A 799 PRO cc_start: 0.8535 (Cg_exo) cc_final: 0.8231 (Cg_endo) outliers start: 25 outliers final: 22 residues processed: 96 average time/residue: 0.1096 time to fit residues: 13.8166 Evaluate side-chains 94 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 860 CYS Chi-restraints excluded: chain A residue 892 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.160383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139605 restraints weight = 9120.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142067 restraints weight = 5976.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.144743 restraints weight = 4257.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145057 restraints weight = 3211.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145292 restraints weight = 2820.690| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7294 Z= 0.122 Angle : 0.514 8.076 10088 Z= 0.278 Chirality : 0.042 0.155 1172 Planarity : 0.004 0.054 1113 Dihedral : 16.525 101.186 1537 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.57 % Allowed : 17.09 % Favored : 79.35 % 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: -0.86 (0.30), residues: 742 helix: 0.79 (0.34), residues: 236 sheet: -0.81 (0.39), residues: 179 loop : -1.40 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 562 TYR 0.024 0.001 TYR A 669 PHE 0.008 0.001 PHE A 685 TRP 0.008 0.001 TRP A 288 HIS 0.002 0.001 HIS A 855 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 7294) covalent geometry : angle 0.51400 / 0.28 (10088) hydrogen bonds : bond 0.03834 / 2.62 ( 269) hydrogen bonds : angle 5.08361 / 3.39 ( 752) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.268 Fit side-chains REVERT: A 189 MET cc_start: 0.7640 (tmm) cc_final: 0.7341 (tmm) REVERT: A 316 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7438 (t70) REVERT: A 567 ASP cc_start: 0.6636 (t0) cc_final: 0.6409 (t0) REVERT: A 799 PRO cc_start: 0.8466 (Cg_exo) cc_final: 0.8145 (Cg_endo) outliers start: 24 outliers final: 19 residues processed: 101 average time/residue: 0.1000 time to fit residues: 13.4199 Evaluate side-chains 95 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 854 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 0.0570 chunk 31 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.159958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.138903 restraints weight = 9042.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141394 restraints weight = 5781.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.143978 restraints weight = 4106.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.144415 restraints weight = 3141.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.144726 restraints weight = 2734.621| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7294 Z= 0.129 Angle : 0.524 6.698 10088 Z= 0.282 Chirality : 0.042 0.167 1172 Planarity : 0.004 0.046 1113 Dihedral : 16.421 100.039 1537 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.57 % Allowed : 17.38 % Favored : 79.05 % 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: -0.83 (0.30), residues: 742 helix: 0.81 (0.34), residues: 236 sheet: -0.79 (0.38), residues: 179 loop : -1.38 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 185 TYR 0.009 0.001 TYR A 298 PHE 0.006 0.001 PHE A 370 TRP 0.006 0.001 TRP A 533 HIS 0.003 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7294) covalent geometry : angle 0.52423 / 0.28 (10088) hydrogen bonds : bond 0.03856 / 2.66 ( 269) hydrogen bonds : angle 4.98101 / 3.32 ( 752) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.253 Fit side-chains REVERT: A 189 MET cc_start: 0.7581 (tmm) cc_final: 0.7314 (tmm) REVERT: A 316 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7421 (t70) REVERT: A 567 ASP cc_start: 0.6677 (t0) cc_final: 0.6416 (t0) REVERT: A 799 PRO cc_start: 0.8480 (Cg_exo) cc_final: 0.8172 (Cg_endo) REVERT: A 811 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7301 (pt0) outliers start: 24 outliers final: 19 residues processed: 96 average time/residue: 0.1023 time to fit residues: 12.9649 Evaluate side-chains 96 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 860 CYS Chi-restraints excluded: chain A residue 892 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.156581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136163 restraints weight = 9068.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139031 restraints weight = 5725.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.141204 restraints weight = 3895.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.141556 restraints weight = 3015.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.141852 restraints weight = 2660.638| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7294 Z= 0.141 Angle : 0.524 6.497 10088 Z= 0.281 Chirality : 0.042 0.161 1172 Planarity : 0.004 0.043 1113 Dihedral : 16.304 98.495 1537 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.71 % Allowed : 17.83 % Favored : 78.45 % 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: -0.79 (0.30), residues: 742 helix: 0.87 (0.34), residues: 234 sheet: -0.78 (0.38), residues: 179 loop : -1.36 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 562 TYR 0.010 0.001 TYR A 350 PHE 0.007 0.001 PHE A 370 TRP 0.008 0.001 TRP E 103 HIS 0.003 0.001 HIS A 855 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 7294) covalent geometry : angle 0.52350 / 0.28 (10088) hydrogen bonds : bond 0.03871 / 2.68 ( 269) hydrogen bonds : angle 4.96360 / 3.31 ( 752) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.256 Fit side-chains REVERT: A 316 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7311 (t70) REVERT: A 567 ASP cc_start: 0.6653 (t0) cc_final: 0.6390 (t0) REVERT: A 799 PRO cc_start: 0.8492 (Cg_exo) cc_final: 0.8192 (Cg_endo) REVERT: A 811 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7254 (pt0) outliers start: 25 outliers final: 22 residues processed: 100 average time/residue: 0.1070 time to fit residues: 14.0356 Evaluate side-chains 104 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 860 CYS Chi-restraints excluded: chain A residue 892 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.157787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.135754 restraints weight = 9073.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138706 restraints weight = 5718.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140809 restraints weight = 4118.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.142190 restraints weight = 3239.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.143184 restraints weight = 2727.155| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7294 Z= 0.170 Angle : 0.551 8.432 10088 Z= 0.294 Chirality : 0.043 0.187 1172 Planarity : 0.004 0.043 1113 Dihedral : 16.113 95.719 1537 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.57 % Allowed : 18.42 % Favored : 78.01 % 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: -0.87 (0.30), residues: 742 helix: 0.78 (0.34), residues: 234 sheet: -0.90 (0.38), residues: 179 loop : -1.33 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 562 TYR 0.012 0.001 TYR A 350 PHE 0.007 0.001 PHE A 370 TRP 0.009 0.001 TRP A 533 HIS 0.003 0.001 HIS A 855 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 7294) covalent geometry : angle 0.55123 / 0.29 (10088) hydrogen bonds : bond 0.04121 / 2.86 ( 269) hydrogen bonds : angle 5.01934 / 3.34 ( 752) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.234 Fit side-chains REVERT: A 316 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7361 (t70) REVERT: A 567 ASP cc_start: 0.6642 (t0) cc_final: 0.6384 (t0) REVERT: A 799 PRO cc_start: 0.8509 (Cg_exo) cc_final: 0.8223 (Cg_endo) REVERT: A 811 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7259 (pt0) outliers start: 24 outliers final: 22 residues processed: 98 average time/residue: 0.1011 time to fit residues: 13.0551 Evaluate side-chains 101 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 238 CYS Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 860 CYS Chi-restraints excluded: chain A residue 892 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 13 optimal weight: 0.0770 chunk 71 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.161648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.139869 restraints weight = 9024.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.142963 restraints weight = 5555.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145079 restraints weight = 3927.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.146339 restraints weight = 3071.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.147414 restraints weight = 2597.457| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7294 Z= 0.108 Angle : 0.502 7.559 10088 Z= 0.270 Chirality : 0.041 0.163 1172 Planarity : 0.004 0.041 1113 Dihedral : 16.065 93.113 1537 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.82 % Allowed : 19.47 % Favored : 77.71 % 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: -0.67 (0.30), residues: 742 helix: 0.99 (0.35), residues: 234 sheet: -0.75 (0.38), residues: 178 loop : -1.27 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 562 TYR 0.010 0.001 TYR A 669 PHE 0.006 0.001 PHE A 201 TRP 0.010 0.001 TRP A 288 HIS 0.003 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7294) covalent geometry : angle 0.50181 / 0.27 (10088) hydrogen bonds : bond 0.03524 / 2.38 ( 269) hydrogen bonds : angle 4.81936 / 3.22 ( 752) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.305 Fit side-chains REVERT: A 567 ASP cc_start: 0.6495 (t0) cc_final: 0.6237 (t0) REVERT: A 697 TYR cc_start: 0.7395 (t80) cc_final: 0.7154 (t80) REVERT: A 799 PRO cc_start: 0.8384 (Cg_exo) cc_final: 0.8084 (Cg_endo) REVERT: A 811 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7215 (pt0) outliers start: 19 outliers final: 16 residues processed: 101 average time/residue: 0.1025 time to fit residues: 13.7158 Evaluate side-chains 94 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 860 CYS Chi-restraints excluded: chain A residue 892 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.161280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140289 restraints weight = 8970.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.143354 restraints weight = 5674.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.145591 restraints weight = 3837.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.145939 restraints weight = 3016.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.146309 restraints weight = 2652.202| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7294 Z= 0.122 Angle : 0.511 7.483 10088 Z= 0.275 Chirality : 0.041 0.157 1172 Planarity : 0.004 0.041 1113 Dihedral : 15.941 92.567 1537 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.67 % Allowed : 20.06 % Favored : 77.27 % 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: -0.69 (0.31), residues: 742 helix: 0.95 (0.34), residues: 236 sheet: -0.82 (0.38), residues: 179 loop : -1.24 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 785 TYR 0.009 0.001 TYR A 298 PHE 0.006 0.001 PHE A 370 TRP 0.008 0.001 TRP A 533 HIS 0.003 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 7294) covalent geometry : angle 0.51136 / 0.27 (10088) hydrogen bonds : bond 0.03593 / 2.45 ( 269) hydrogen bonds : angle 4.84557 / 3.23 ( 752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1235.75 seconds wall clock time: 22 minutes 15.10 seconds (1335.10 seconds total)