Starting phenix.real_space_refine on Tue Aug 4 22:46:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nhb_49407/08_2026/9nhb_49407.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nhb_49407/08_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_49407/08_2026/9nhb_49407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nhb_49407/08_2026/9nhb_49407.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nhb_49407/08_2026/9nhb_49407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nhb_49407/08_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.35, per 1000 atoms: 0.19 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: 0.54 Conformation dependent library (CDL) restraints added in 317.1 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: 0.74 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: 0.97 Time building geometry restraints manager: 0.76 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=" C5' A C 20 " pdb=" C4' A C 20 " ideal model delta sigma weight residual 1.508 1.567 -0.059 7.00e-03 2.04e+04 7.12e+01 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 ... (remaining 7289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 9684 3.51 - 7.02: 386 7.02 - 10.53: 12 10.53 - 14.04: 4 14.04 - 17.55: 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 119.70 102.15 17.55 1.20e+00 6.94e-01 2.14e+02 angle pdb=" O5' A C 20 " pdb=" C5' A C 20 " pdb=" C4' A C 20 " ideal model delta sigma weight residual 109.40 120.03 -10.63 8.00e-01 1.56e+00 1.77e+02 angle pdb=" C3' U B 21 " pdb=" O3' U B 21 " pdb=" P G B 22 " ideal model delta sigma weight residual 119.70 106.68 13.02 1.20e+00 6.94e-01 1.18e+02 angle pdb=" C3' U B 20 " pdb=" O3' U B 20 " pdb=" P U B 21 " ideal model delta sigma weight residual 119.70 107.11 12.59 1.20e+00 6.94e-01 1.10e+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 ... (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: 1003 0.118 - 0.236: 137 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: 1.750 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.340 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: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.640 ------------------------------------------------------------------------------- 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= 0.666 Angle : 1.539 17.546 10088 Z= 1.142 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 0.00979 / 0.67 ( 7294) covalent geometry : angle 1.53940 / 1.14 (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 : 0.306 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 113 average time/residue: 0.1150 time to fit residues: 16.5571 Evaluate side-chains 71 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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: 5.9990 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 = 0.3893 r_free = 0.3893 target = 0.163517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.142538 restraints weight = 8967.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.146359 restraints weight = 5962.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.147009 restraints weight = 3708.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.147924 restraints weight = 3512.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.148031 restraints weight = 2977.529| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7294 Z= 0.147 Angle : 0.628 9.260 10088 Z= 0.337 Chirality : 0.045 0.182 1172 Planarity : 0.005 0.040 1113 Dihedral : 16.957 101.715 1537 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: -1.05 (0.30), residues: 742 helix: 0.58 (0.34), residues: 228 sheet: -1.06 (0.37), residues: 187 loop : -1.32 (0.33), residues: 327 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 0.011 0.001 PHE A 775 TRP 0.013 0.002 TRP A 166 HIS 0.005 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 7294) covalent geometry : angle 0.62776 / 0.34 (10088) hydrogen bonds : bond 0.05447 / 3.74 ( 269) hydrogen bonds : angle 5.79815 / 3.89 ( 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 95 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.7381 (ttp) cc_final: 0.6842 (tmm) REVERT: A 234 ILE cc_start: 0.8947 (mt) cc_final: 0.8639 (tt) REVERT: A 779 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8289 (p) REVERT: A 799 PRO cc_start: 0.8583 (Cg_exo) cc_final: 0.8180 (Cg_endo) outliers start: 14 outliers final: 12 residues processed: 90 average time/residue: 0.0966 time to fit residues: 11.2678 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 : 0.243 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.156925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.136269 restraints weight = 8968.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138992 restraints weight = 5662.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.140833 restraints weight = 4097.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.142002 restraints weight = 3251.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.143028 restraints weight = 2763.129| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7294 Z= 0.183 Angle : 0.598 6.976 10088 Z= 0.319 Chirality : 0.044 0.171 1172 Planarity : 0.005 0.038 1113 Dihedral : 16.563 101.694 1537 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.57 % Allowed : 14.12 % 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: -1.01 (0.30), residues: 742 helix: 0.63 (0.34), residues: 234 sheet: -0.95 (0.38), residues: 179 loop : -1.41 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 353 TYR 0.020 0.002 TYR A 669 PHE 0.011 0.001 PHE A 370 TRP 0.012 0.002 TRP A 533 HIS 0.005 0.001 HIS A 855 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 7294) covalent geometry : angle 0.59821 / 0.32 (10088) hydrogen bonds : bond 0.05075 / 3.58 ( 269) hydrogen bonds : angle 5.45841 / 3.65 ( 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: 24 poor density : 85 time to evaluate : 0.234 Fit side-chains REVERT: A 189 MET cc_start: 0.7632 (ttp) cc_final: 0.7421 (tmm) REVERT: A 669 TYR cc_start: 0.7458 (m-10) cc_final: 0.6419 (m-80) REVERT: A 799 PRO cc_start: 0.8577 (Cg_exo) cc_final: 0.8230 (Cg_endo) outliers start: 24 outliers final: 16 residues processed: 102 average time/residue: 0.0912 time to fit residues: 12.2112 Evaluate side-chains 91 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 42 optimal weight: 0.0050 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.159356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137896 restraints weight = 9105.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.140809 restraints weight = 5749.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142780 restraints weight = 4155.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.144136 restraints weight = 3298.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.144928 restraints weight = 2788.744| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2072 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= 0.160 Angle : 0.558 8.498 10088 Z= 0.299 Chirality : 0.043 0.158 1172 Planarity : 0.004 0.036 1113 Dihedral : 16.464 99.777 1537 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.27 % Allowed : 16.49 % Favored : 80.24 % 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: -0.96 (0.30), residues: 742 helix: 0.71 (0.35), residues: 234 sheet: -0.78 (0.39), residues: 173 loop : -1.50 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 739 TYR 0.025 0.001 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 0.00372 / 0.16 ( 7294) covalent geometry : angle 0.55759 / 0.30 (10088) hydrogen bonds : bond 0.04422 / 3.02 ( 269) hydrogen bonds : angle 5.28641 / 3.53 ( 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 104 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.188 Fit side-chains REVERT: A 567 ASP cc_start: 0.6668 (t0) cc_final: 0.6450 (t0) REVERT: A 799 PRO cc_start: 0.8512 (Cg_exo) cc_final: 0.8176 (Cg_endo) outliers start: 22 outliers final: 18 residues processed: 98 average time/residue: 0.0812 time to fit residues: 10.4455 Evaluate side-chains 94 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 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 599 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 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: 1.9990 chunk 48 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.156051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.134869 restraints weight = 9098.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137607 restraints weight = 5938.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139870 restraints weight = 4176.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140200 restraints weight = 3279.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.140360 restraints weight = 2886.333| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7294 Z= 0.207 Angle : 0.600 7.066 10088 Z= 0.318 Chirality : 0.045 0.162 1172 Planarity : 0.005 0.037 1113 Dihedral : 16.337 98.782 1537 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.01 % Allowed : 16.49 % Favored : 79.49 % 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: 0.56 (0.35), residues: 235 sheet: -1.00 (0.39), residues: 179 loop : -1.53 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 390 TYR 0.026 0.002 TYR A 669 PHE 0.009 0.001 PHE A 370 TRP 0.012 0.001 TRP A 533 HIS 0.005 0.001 HIS A 855 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 ( 7294) covalent geometry : angle 0.60010 / 0.32 (10088) hydrogen bonds : bond 0.04707 / 3.31 ( 269) hydrogen bonds : angle 5.33468 / 3.55 ( 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 103 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.243 Fit side-chains REVERT: A 316 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7521 (t70) REVERT: A 567 ASP cc_start: 0.6756 (t0) cc_final: 0.6503 (t0) REVERT: A 799 PRO cc_start: 0.8572 (Cg_exo) cc_final: 0.8275 (Cg_endo) outliers start: 27 outliers final: 21 residues processed: 96 average time/residue: 0.0987 time to fit residues: 12.3594 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 : 0.221 ------------------------------------------------------------------------------- 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 316 ASP 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 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: 3.9990 chunk 58 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.159505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138876 restraints weight = 9096.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141367 restraints weight = 5913.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143740 restraints weight = 4199.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.144097 restraints weight = 3268.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144433 restraints weight = 2858.934| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7294 Z= 0.125 Angle : 0.528 7.859 10088 Z= 0.283 Chirality : 0.042 0.155 1172 Planarity : 0.004 0.035 1113 Dihedral : 16.358 98.981 1537 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.86 % Allowed : 16.94 % Favored : 79.20 % 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: -0.92 (0.30), residues: 742 helix: 0.65 (0.34), residues: 236 sheet: -0.70 (0.40), residues: 173 loop : -1.45 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 562 TYR 0.028 0.001 TYR A 669 PHE 0.009 0.001 PHE A 685 TRP 0.008 0.001 TRP A 288 HIS 0.003 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 7294) covalent geometry : angle 0.52773 / 0.28 (10088) hydrogen bonds : bond 0.04027 / 2.75 ( 269) hydrogen bonds : angle 5.08257 / 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 109 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.172 Fit side-chains REVERT: A 316 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7452 (t70) REVERT: A 567 ASP cc_start: 0.6648 (t0) cc_final: 0.6372 (t0) REVERT: A 799 PRO cc_start: 0.8479 (Cg_exo) cc_final: 0.8162 (Cg_endo) REVERT: A 811 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6737 (pm20) outliers start: 26 outliers final: 20 residues processed: 105 average time/residue: 0.0895 time to fit residues: 12.4014 Evaluate side-chains 100 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 0.0060 chunk 31 optimal weight: 0.9980 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: 0.8980 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.0170 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.5234 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.161471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.140909 restraints weight = 8986.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143194 restraints weight = 5851.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.145959 restraints weight = 4212.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.146265 restraints weight = 3154.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.146346 restraints weight = 2747.761| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7294 Z= 0.110 Angle : 0.510 7.368 10088 Z= 0.272 Chirality : 0.041 0.157 1172 Planarity : 0.004 0.053 1113 Dihedral : 16.267 98.083 1537 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.12 % Allowed : 18.87 % 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: -0.77 (0.30), residues: 742 helix: 0.84 (0.34), residues: 236 sheet: -0.66 (0.39), residues: 178 loop : -1.40 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 562 TYR 0.009 0.001 TYR A 669 PHE 0.006 0.001 PHE A 370 TRP 0.007 0.001 TRP E 103 HIS 0.003 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 7294) covalent geometry : angle 0.51018 / 0.27 (10088) hydrogen bonds : bond 0.03704 / 2.54 ( 269) hydrogen bonds : angle 4.89326 / 3.26 ( 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 105 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.239 Fit side-chains REVERT: A 189 MET cc_start: 0.7151 (tmm) cc_final: 0.6944 (tmm) REVERT: A 567 ASP cc_start: 0.6664 (t0) cc_final: 0.6385 (t0) REVERT: A 799 PRO cc_start: 0.8436 (Cg_exo) cc_final: 0.8120 (Cg_endo) REVERT: A 811 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6712 (pm20) outliers start: 21 outliers final: 18 residues processed: 101 average time/residue: 0.1058 time to fit residues: 13.9564 Evaluate side-chains 97 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL 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 485 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 599 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 835 ILE Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 854 THR 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: 1.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 27 optimal weight: 0.0970 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.160361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139400 restraints weight = 9039.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.142039 restraints weight = 5756.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.143090 restraints weight = 4355.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.143859 restraints weight = 3476.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144736 restraints weight = 3031.137| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7294 Z= 0.134 Angle : 0.522 6.790 10088 Z= 0.277 Chirality : 0.042 0.179 1172 Planarity : 0.004 0.049 1113 Dihedral : 16.165 96.283 1537 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.27 % Allowed : 19.02 % 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: -0.75 (0.30), residues: 742 helix: 0.87 (0.34), residues: 236 sheet: -0.71 (0.38), residues: 177 loop : -1.35 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 562 TYR 0.010 0.001 TYR A 350 PHE 0.007 0.001 PHE A 370 TRP 0.007 0.001 TRP A 533 HIS 0.003 0.001 HIS A 855 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 7294) covalent geometry : angle 0.52210 / 0.28 (10088) hydrogen bonds : bond 0.03839 / 2.66 ( 269) hydrogen bonds : angle 4.91465 / 3.28 ( 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 100 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.223 Fit side-chains REVERT: A 189 MET cc_start: 0.7249 (tmm) cc_final: 0.7048 (tmm) REVERT: A 316 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7343 (t70) REVERT: A 543 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6515 (mtm180) REVERT: A 567 ASP cc_start: 0.6633 (t0) cc_final: 0.6343 (t0) REVERT: A 799 PRO cc_start: 0.8487 (Cg_exo) cc_final: 0.8192 (Cg_endo) REVERT: A 811 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6729 (pm20) outliers start: 22 outliers final: 19 residues processed: 98 average time/residue: 0.1079 time to fit residues: 13.6402 Evaluate side-chains 99 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE 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 360 VAL 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 543 ARG 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 892 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 65 optimal weight: 0.0030 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.158367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136681 restraints weight = 9010.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139714 restraints weight = 5588.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141718 restraints weight = 3975.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.143020 restraints weight = 3136.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143961 restraints weight = 2654.110| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7294 Z= 0.156 Angle : 0.538 6.609 10088 Z= 0.285 Chirality : 0.042 0.156 1172 Planarity : 0.004 0.046 1113 Dihedral : 15.987 93.207 1537 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.57 % Allowed : 18.87 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.30), residues: 742 helix: 0.86 (0.34), residues: 234 sheet: -0.82 (0.38), residues: 177 loop : -1.35 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 562 TYR 0.011 0.001 TYR A 350 PHE 0.007 0.001 PHE A 370 TRP 0.008 0.001 TRP A 533 HIS 0.003 0.001 HIS A 855 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 7294) covalent geometry : angle 0.53824 / 0.28 (10088) hydrogen bonds : bond 0.04003 / 2.78 ( 269) hydrogen bonds : angle 4.95967 / 3.31 ( 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 : 0.255 Fit side-chains REVERT: A 316 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7371 (t70) REVERT: A 543 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6407 (mtm180) REVERT: A 567 ASP cc_start: 0.6670 (t0) cc_final: 0.6391 (t0) REVERT: A 799 PRO cc_start: 0.8490 (Cg_exo) cc_final: 0.8207 (Cg_endo) REVERT: A 811 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6717 (pm20) outliers start: 24 outliers final: 20 residues processed: 99 average time/residue: 0.1097 time to fit residues: 13.9441 Evaluate side-chains 101 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE 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 360 VAL 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 543 ARG 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: 0.5980 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 44 optimal weight: 0.0020 chunk 13 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.161797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.140718 restraints weight = 9036.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.143691 restraints weight = 5772.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144725 restraints weight = 4177.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.145485 restraints weight = 3398.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.145647 restraints weight = 2957.467| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2729 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 : 0.514 7.985 10088 Z= 0.271 Chirality : 0.041 0.143 1172 Planarity : 0.004 0.044 1113 Dihedral : 15.954 90.731 1537 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.12 % Allowed : 19.32 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.31), residues: 742 helix: 0.99 (0.35), residues: 234 sheet: -0.75 (0.39), 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 0.009 0.001 TYR A 298 PHE 0.005 0.001 PHE A 370 TRP 0.007 0.001 TRP A 288 HIS 0.003 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 7294) covalent geometry : angle 0.51364 / 0.27 (10088) hydrogen bonds : bond 0.03603 / 2.45 ( 269) hydrogen bonds : angle 4.83833 / 3.24 ( 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 103 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.237 Fit side-chains REVERT: A 316 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7318 (t70) REVERT: A 543 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6541 (mtm180) REVERT: A 567 ASP cc_start: 0.6679 (t0) cc_final: 0.6406 (t0) REVERT: A 799 PRO cc_start: 0.8426 (Cg_exo) cc_final: 0.8132 (Cg_endo) REVERT: A 811 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6709 (pm20) outliers start: 21 outliers final: 18 residues processed: 100 average time/residue: 0.1059 time to fit residues: 13.7312 Evaluate side-chains 98 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 VAL 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 543 ARG Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 630 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 827 ILE Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 854 THR 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: 0.9980 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 0.0370 chunk 42 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 = 0.161650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.140749 restraints weight = 8960.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.143354 restraints weight = 5694.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.144425 restraints weight = 4330.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.145128 restraints weight = 3468.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145366 restraints weight = 3021.020| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2786 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= 0.120 Angle : 0.520 10.137 10088 Z= 0.273 Chirality : 0.041 0.155 1172 Planarity : 0.004 0.043 1113 Dihedral : 15.843 88.834 1537 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.12 % Allowed : 19.61 % 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: -0.67 (0.31), residues: 742 helix: 0.95 (0.34), residues: 236 sheet: -0.75 (0.38), residues: 179 loop : -1.24 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 562 TYR 0.009 0.001 TYR A 298 PHE 0.006 0.001 PHE A 201 TRP 0.007 0.001 TRP A 533 HIS 0.003 0.001 HIS A 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 7294) covalent geometry : angle 0.51965 / 0.27 (10088) hydrogen bonds : bond 0.03574 / 2.45 ( 269) hydrogen bonds : angle 4.81244 / 3.22 ( 752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1144.68 seconds wall clock time: 20 minutes 33.77 seconds (1233.77 seconds total)