Starting phenix.real_space_refine on Fri Oct 23 02:56:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izr_61040/10_2026/9izr_61040.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izr_61040/10_2026/9izr_61040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9izr_61040/10_2026/9izr_61040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izr_61040/10_2026/9izr_61040.map" model { file = "/net/cci-nas-00/data/ceres_data/9izr_61040/10_2026/9izr_61040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izr_61040/10_2026/9izr_61040.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 sd= 0.208 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 98 5.49 5 Mg 8 5.21 5 S 36 5.16 5 C 4878 2.51 5 N 1378 2.21 5 O 1802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8200 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 6133 Classifications: {'peptide': 738} Link IDs: {'PTRANS': 12, 'TRANS': 725} Chain: "B" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1127 Classifications: {'RNA': 53} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 24, 'rna3p_pyr': 20} Link IDs: {'rna2p': 9, 'rna3p': 43} Chain: "C" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 265 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 545 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 125 Unusual residues: {' AS': 2, ' GS': 1, ' MG': 3, ' SC': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" 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: 1.87, per 1000 atoms: 0.23 Number of scatterers: 8200 At special positions: 0 Unit cell: (92.13, 98.355, 110.805, 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 36 16.00 P 98 15.00 Mg 8 11.99 O 1802 8.00 N 1378 7.00 C 4878 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 244.5 milliseconds 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 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: 31 helices and 6 sheets defined 53.7% alpha, 9.8% beta 33 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 16 through 37 removed outlier: 3.568A pdb=" N ILE A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.718A pdb=" N PHE A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 119 through 134 removed outlier: 3.567A pdb=" N LEU A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 169 through 181 removed outlier: 3.618A pdb=" N ASP A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.751A pdb=" N ASN A 191 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 219 Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.682A pdb=" N ASP A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 354 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 363 through 375 removed outlier: 3.622A pdb=" N LYS A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 397 through 418 Processing helix chain 'A' and resid 420 through 459 removed outlier: 3.523A pdb=" N ALA A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 479 through 482 Processing helix chain 'A' and resid 483 through 518 removed outlier: 3.612A pdb=" N GLU A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 564 through 571 removed outlier: 3.556A pdb=" N TYR A 568 " --> pdb=" O LYS A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.526A pdb=" N LYS A 596 " --> pdb=" O LYS A 592 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET A 607 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS A 608 " --> pdb=" O ASN A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 613 No H-bonds generated for 'chain 'A' and resid 611 through 613' Processing helix chain 'A' and resid 614 through 626 removed outlier: 4.370A pdb=" N ASN A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 678 through 693 removed outlier: 3.730A pdb=" N ALA A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 701 removed outlier: 3.746A pdb=" N GLU A 698 " --> pdb=" O GLU A 694 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.579A pdb=" N MET A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 731 " --> pdb=" O MET A 727 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.765A pdb=" N ILE A 5 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER A 305 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN A 290 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 242 through 245 Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 321 removed outlier: 6.731A pdb=" N VAL A 321 " --> pdb=" O ALA A 524 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N GLU A 526 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL A 523 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL A 633 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A 525 " --> pdb=" O VAL A 633 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 325 removed outlier: 7.794A pdb=" N THR A 334 " --> pdb=" O PHE A 379 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N PHE A 379 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU A 336 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 641 through 642 removed outlier: 3.601A pdb=" N CYS A 647 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 641 through 642 removed outlier: 3.601A pdb=" N CYS A 647 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU A 648 " --> pdb=" O LYS A 735 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 3390 1.39 - 1.57: 4913 1.57 - 1.75: 188 1.75 - 1.93: 52 1.93 - 2.11: 1 Bond restraints: 8544 Sorted by residual: bond pdb=" C3' DA D 24 " pdb=" C2' DA D 24 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.62e+00 bond pdb=" O5' GS A 804 " pdb=" P GS A 804 " ideal model delta sigma weight residual 1.632 1.572 0.060 2.00e-02 2.50e+03 9.07e+00 bond pdb=" C3' DT C -3 " pdb=" C2' DT C -3 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.71e+00 bond pdb=" C3' DC D 19 " pdb=" C2' DC D 19 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.24e+00 bond pdb=" C3' DA D 23 " pdb=" C2' DA D 23 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.17e+00 ... (remaining 8539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 11530 1.77 - 3.55: 373 3.55 - 5.32: 22 5.32 - 7.09: 6 7.09 - 8.86: 1 Bond angle restraints: 11932 Sorted by residual: angle pdb=" C ASP A 654 " pdb=" CA ASP A 654 " pdb=" CB ASP A 654 " ideal model delta sigma weight residual 116.54 110.53 6.01 1.15e+00 7.56e-01 2.73e+01 angle pdb=" O4' DG D 8 " pdb=" C4' DG D 8 " pdb=" C3' DG D 8 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.48e+01 angle pdb=" N3 DT D 13 " pdb=" C4 DT D 13 " pdb=" O4 DT D 13 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT C -3 " pdb=" C4 DT C -3 " pdb=" O4 DT C -3 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT C -8 " pdb=" C4 DT C -8 " pdb=" O4 DT C -8 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 11927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.29: 4456 19.29 - 38.58: 428 38.58 - 57.87: 236 57.87 - 77.16: 89 77.16 - 96.45: 4 Dihedral angle restraints: 5213 sinusoidal: 3006 harmonic: 2207 Sorted by residual: dihedral pdb=" CA SER A 4 " pdb=" C SER A 4 " pdb=" N ILE A 5 " pdb=" CA ILE A 5 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ARG A 420 " pdb=" C ARG A 420 " pdb=" N THR A 421 " pdb=" CA THR A 421 " ideal model delta harmonic sigma weight residual -180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASN A 285 " pdb=" C ASN A 285 " pdb=" N THR A 286 " pdb=" CA THR A 286 " ideal model delta harmonic sigma weight residual -180.00 -162.84 -17.16 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 989 0.049 - 0.099: 275 0.099 - 0.148: 82 0.148 - 0.197: 3 0.197 - 0.246: 1 Chirality restraints: 1350 Sorted by residual: chirality pdb=" C3' SC A 807 " pdb=" C2' SC A 807 " pdb=" C4' SC A 807 " pdb=" O3' SC A 807 " both_signs ideal model delta sigma weight residual False -2.56 -2.81 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1' G B 1 " pdb=" O4' G B 1 " pdb=" C2' G B 1 " pdb=" N9 G B 1 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" C3' SC A 808 " pdb=" C2' SC A 808 " pdb=" C4' SC A 808 " pdb=" O3' SC A 808 " both_signs ideal model delta sigma weight residual False -2.56 -2.74 0.18 2.00e-01 2.50e+01 7.69e-01 ... (remaining 1347 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' AS A 806 " 0.078 2.00e-02 2.50e+03 3.16e-02 2.75e+01 pdb=" C2 AS A 806 " -0.004 2.00e-02 2.50e+03 pdb=" C4 AS A 806 " -0.031 2.00e-02 2.50e+03 pdb=" C5 AS A 806 " -0.017 2.00e-02 2.50e+03 pdb=" C6 AS A 806 " 0.007 2.00e-02 2.50e+03 pdb=" C8 AS A 806 " -0.018 2.00e-02 2.50e+03 pdb=" N1 AS A 806 " 0.012 2.00e-02 2.50e+03 pdb=" N3 AS A 806 " -0.027 2.00e-02 2.50e+03 pdb=" N6 AS A 806 " 0.039 2.00e-02 2.50e+03 pdb=" N7 AS A 806 " -0.010 2.00e-02 2.50e+03 pdb=" N9 AS A 806 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' SC A 808 " 0.054 2.00e-02 2.50e+03 2.60e-02 1.52e+01 pdb=" C2 SC A 808 " -0.012 2.00e-02 2.50e+03 pdb=" C4 SC A 808 " -0.001 2.00e-02 2.50e+03 pdb=" C5 SC A 808 " -0.018 2.00e-02 2.50e+03 pdb=" C6 SC A 808 " -0.027 2.00e-02 2.50e+03 pdb=" N1 SC A 808 " -0.013 2.00e-02 2.50e+03 pdb=" N3 SC A 808 " -0.002 2.00e-02 2.50e+03 pdb=" N4 SC A 808 " 0.037 2.00e-02 2.50e+03 pdb=" O2 SC A 808 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GS A 804 " -0.044 2.00e-02 2.50e+03 1.82e-02 9.97e+00 pdb=" C2 GS A 804 " 0.010 2.00e-02 2.50e+03 pdb=" C4 GS A 804 " 0.016 2.00e-02 2.50e+03 pdb=" C5 GS A 804 " 0.008 2.00e-02 2.50e+03 pdb=" C6 GS A 804 " -0.003 2.00e-02 2.50e+03 pdb=" C8 GS A 804 " 0.010 2.00e-02 2.50e+03 pdb=" N1 GS A 804 " 0.002 2.00e-02 2.50e+03 pdb=" N2 GS A 804 " -0.011 2.00e-02 2.50e+03 pdb=" N3 GS A 804 " 0.020 2.00e-02 2.50e+03 pdb=" N7 GS A 804 " 0.004 2.00e-02 2.50e+03 pdb=" N9 GS A 804 " 0.016 2.00e-02 2.50e+03 pdb=" O6 GS A 804 " -0.026 2.00e-02 2.50e+03 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 37 2.39 - 3.02: 4405 3.02 - 3.65: 12364 3.65 - 4.27: 20983 4.27 - 4.90: 31569 Nonbonded interactions: 69358 Sorted by model distance: nonbonded pdb=" OE2 GLU A 526 " pdb="MG MG A 802 " model vdw 1.765 2.170 nonbonded pdb=" OP2 U B -31 " pdb="MG MG B 103 " model vdw 1.973 2.170 nonbonded pdb=" OD1 ASP A 324 " pdb="MG MG A 802 " model vdw 2.039 2.170 nonbonded pdb=" O HIS A 329 " pdb=" OH TYR A 349 " model vdw 2.056 3.040 nonbonded pdb=" OD2 ASP A 324 " pdb="MG MG A 803 " model vdw 2.063 2.170 ... (remaining 69353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.050 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.570 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8549 Z= 0.351 Angle : 0.666 8.864 11932 Z= 0.490 Chirality : 0.049 0.246 1350 Planarity : 0.003 0.032 1167 Dihedral : 19.415 96.453 3787 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.87 % Allowed : 4.07 % Favored : 95.06 % 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: -0.11 (0.31), residues: 736 helix: 0.49 (0.27), residues: 358 sheet: -0.02 (0.62), residues: 76 loop : -0.66 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 475 TYR 0.018 0.002 TYR A 60 PHE 0.015 0.002 PHE A 602 TRP 0.010 0.002 TRP A 696 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.35 ( 8544) covalent geometry : angle 0.66599 / 0.49 (11932) hydrogen bonds : bond 0.17957 / 10.96 ( 357) hydrogen bonds : angle 5.60089 / 3.85 ( 957) Misc. bond : bond 0.02138 / 1.19 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 198 LYS cc_start: 0.7807 (mttt) cc_final: 0.7222 (mtpp) REVERT: A 326 ASN cc_start: 0.7630 (m-40) cc_final: 0.7254 (m110) REVERT: A 420 ARG cc_start: 0.6854 (mtp180) cc_final: 0.6618 (mtm180) REVERT: A 494 ASN cc_start: 0.8563 (m-40) cc_final: 0.8342 (m-40) REVERT: A 547 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7566 (mtpt) REVERT: A 627 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8009 (pttp) REVERT: A 680 ASP cc_start: 0.6108 (m-30) cc_final: 0.5812 (m-30) outliers start: 6 outliers final: 2 residues processed: 145 average time/residue: 0.5858 time to fit residues: 89.9657 Evaluate side-chains 93 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 421 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.0020 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 overall best weight: 1.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS A 156 GLN A 167 ASN A 218 GLN A 259 ASN A 498 GLN A 506 ASN A 537 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.163547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130848 restraints weight = 10149.371| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.59 r_work: 0.3405 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8549 Z= 0.169 Angle : 0.606 8.875 11932 Z= 0.341 Chirality : 0.042 0.188 1350 Planarity : 0.004 0.036 1167 Dihedral : 21.798 93.792 2184 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.76 % Allowed : 12.65 % Favored : 84.59 % 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: 0.03 (0.31), residues: 736 helix: 0.71 (0.27), residues: 363 sheet: -0.03 (0.59), residues: 77 loop : -0.74 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 141 TYR 0.027 0.002 TYR A 437 PHE 0.016 0.002 PHE A 603 TRP 0.008 0.001 TRP A 33 HIS 0.005 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 ( 8544) covalent geometry : angle 0.60591 / 0.34 (11932) hydrogen bonds : bond 0.05960 / 3.89 ( 357) hydrogen bonds : angle 4.31349 / 2.96 ( 957) Misc. bond : bond 0.00303 / 0.17 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8848 (mttt) cc_final: 0.8104 (tptp) REVERT: A 197 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7155 (ttm-80) REVERT: A 317 PHE cc_start: 0.7641 (m-80) cc_final: 0.7377 (m-80) REVERT: A 326 ASN cc_start: 0.7513 (m-40) cc_final: 0.7032 (m110) REVERT: A 331 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7022 (m-80) REVERT: A 356 ASP cc_start: 0.7896 (m-30) cc_final: 0.7447 (m-30) REVERT: A 360 ASN cc_start: 0.8542 (m-40) cc_final: 0.8318 (m-40) REVERT: A 366 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7920 (mt-10) REVERT: A 494 ASN cc_start: 0.8489 (m-40) cc_final: 0.8285 (m-40) REVERT: A 547 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7548 (mtpt) REVERT: A 588 LYS cc_start: 0.8460 (mtpp) cc_final: 0.7947 (ptmm) REVERT: A 627 LYS cc_start: 0.8449 (mtmt) cc_final: 0.7939 (pttp) REVERT: A 680 ASP cc_start: 0.6349 (m-30) cc_final: 0.6002 (m-30) outliers start: 19 outliers final: 8 residues processed: 116 average time/residue: 0.6093 time to fit residues: 74.7827 Evaluate side-chains 93 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 638 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [62, 4, 63, 76, 39, 70, 30, 45, 15, 26, 28] chunk 62 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 ASN ** A 509 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 = 0.3981 r_free = 0.3981 target = 0.161132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127585 restraints weight = 10009.303| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.66 r_work: 0.3356 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8549 Z= 0.247 Angle : 0.636 9.224 11932 Z= 0.348 Chirality : 0.045 0.203 1350 Planarity : 0.004 0.038 1167 Dihedral : 21.628 93.451 2181 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.78 % Allowed : 14.10 % Favored : 82.12 % 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: -0.09 (0.30), residues: 736 helix: 0.69 (0.27), residues: 359 sheet: -0.24 (0.58), residues: 77 loop : -0.84 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 141 TYR 0.028 0.003 TYR A 437 PHE 0.012 0.002 PHE A 252 TRP 0.009 0.002 TRP A 172 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.25 ( 8544) covalent geometry : angle 0.63614 / 0.35 (11932) hydrogen bonds : bond 0.06088 / 4.00 ( 357) hydrogen bonds : angle 4.27786 / 2.95 ( 957) Misc. bond : bond 0.00115 / 0.07 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.8438 (mtpm) cc_final: 0.8144 (mppt) REVERT: A 194 LYS cc_start: 0.8857 (mttt) cc_final: 0.8173 (tptp) REVERT: A 197 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6709 (ttm-80) REVERT: A 210 LYS cc_start: 0.7724 (ttmt) cc_final: 0.7013 (tptt) REVERT: A 273 VAL cc_start: 0.7710 (OUTLIER) cc_final: 0.7437 (m) REVERT: A 326 ASN cc_start: 0.7852 (m-40) cc_final: 0.7380 (m110) REVERT: A 331 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7076 (m-80) REVERT: A 356 ASP cc_start: 0.7988 (m-30) cc_final: 0.7518 (m-30) REVERT: A 360 ASN cc_start: 0.8545 (m-40) cc_final: 0.8299 (m-40) REVERT: A 366 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8027 (mt-10) REVERT: A 547 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7456 (mtpt) REVERT: A 588 LYS cc_start: 0.8417 (mtpp) cc_final: 0.7910 (ptmm) REVERT: A 627 LYS cc_start: 0.8470 (mtmt) cc_final: 0.7991 (pttp) REVERT: A 650 MET cc_start: 0.7228 (mmm) cc_final: 0.6457 (mmp) REVERT: A 680 ASP cc_start: 0.6613 (m-30) cc_final: 0.6240 (m-30) outliers start: 26 outliers final: 11 residues processed: 110 average time/residue: 0.5591 time to fit residues: 65.2912 Evaluate side-chains 96 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 638 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [4, 11, 47, 68, 25, 64, 27, 59, 28, 63, 9] chunk 4 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 59 optimal weight: 0.0870 chunk 28 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 509 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 = 0.4016 r_free = 0.4016 target = 0.164203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131143 restraints weight = 10303.587| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.66 r_work: 0.3405 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8549 Z= 0.143 Angle : 0.547 7.806 11932 Z= 0.310 Chirality : 0.040 0.196 1350 Planarity : 0.003 0.038 1167 Dihedral : 21.343 93.855 2181 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.05 % Allowed : 15.41 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.30), residues: 736 helix: 0.88 (0.27), residues: 363 sheet: -0.20 (0.56), residues: 77 loop : -0.70 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 141 TYR 0.026 0.002 TYR A 437 PHE 0.012 0.001 PHE A 603 TRP 0.007 0.001 TRP A 33 HIS 0.003 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 8544) covalent geometry : angle 0.54712 / 0.31 (11932) hydrogen bonds : bond 0.05087 / 3.38 ( 357) hydrogen bonds : angle 4.08889 / 2.84 ( 957) Misc. bond : bond 0.00127 / 0.08 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8900 (mttt) cc_final: 0.8080 (tptp) REVERT: A 197 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6715 (ttm-80) REVERT: A 199 CYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7414 (t) REVERT: A 206 MET cc_start: 0.6580 (tpp) cc_final: 0.6259 (tpp) REVERT: A 326 ASN cc_start: 0.7699 (m-40) cc_final: 0.7186 (m110) REVERT: A 331 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: A 356 ASP cc_start: 0.7968 (m-30) cc_final: 0.7538 (m-30) REVERT: A 360 ASN cc_start: 0.8551 (m-40) cc_final: 0.8320 (m-40) REVERT: A 366 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7967 (mt-10) REVERT: A 547 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7535 (mmmm) REVERT: A 588 LYS cc_start: 0.8406 (mtpp) cc_final: 0.7913 (ptmm) REVERT: A 627 LYS cc_start: 0.8405 (mtmt) cc_final: 0.7953 (pttp) REVERT: A 650 MET cc_start: 0.7269 (mmm) cc_final: 0.6542 (mmp) REVERT: A 680 ASP cc_start: 0.6607 (m-30) cc_final: 0.6194 (m-30) outliers start: 21 outliers final: 8 residues processed: 103 average time/residue: 0.5933 time to fit residues: 64.8904 Evaluate side-chains 91 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 526 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [36, 80, 51, 0, 37, 65, 62, 20, 44, 46, 21] chunk 36 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 51 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 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 = 0.4002 r_free = 0.4002 target = 0.163104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.129744 restraints weight = 10162.859| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.59 r_work: 0.3396 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8549 Z= 0.183 Angle : 0.568 8.008 11932 Z= 0.318 Chirality : 0.041 0.187 1350 Planarity : 0.003 0.038 1167 Dihedral : 21.141 94.100 2181 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.05 % Allowed : 16.13 % Favored : 80.81 % 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: 0.11 (0.30), residues: 736 helix: 0.89 (0.27), residues: 360 sheet: -0.34 (0.56), residues: 77 loop : -0.72 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 141 TYR 0.026 0.002 TYR A 649 PHE 0.021 0.002 PHE A 603 TRP 0.012 0.002 TRP A 172 HIS 0.004 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 ( 8544) covalent geometry : angle 0.56803 / 0.32 (11932) hydrogen bonds : bond 0.05294 / 3.51 ( 357) hydrogen bonds : angle 4.05370 / 2.81 ( 957) Misc. bond : bond 0.00108 / 0.06 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LYS cc_start: 0.8840 (mttt) cc_final: 0.8083 (tptp) REVERT: A 197 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.6752 (ttm-80) REVERT: A 198 LYS cc_start: 0.7582 (pptt) cc_final: 0.7324 (pptt) REVERT: A 206 MET cc_start: 0.6824 (tpp) cc_final: 0.6556 (tpp) REVERT: A 210 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7642 (mtmt) REVERT: A 273 VAL cc_start: 0.7751 (OUTLIER) cc_final: 0.7488 (m) REVERT: A 317 PHE cc_start: 0.7564 (m-80) cc_final: 0.7321 (m-80) REVERT: A 326 ASN cc_start: 0.7746 (m-40) cc_final: 0.7191 (m110) REVERT: A 331 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: A 356 ASP cc_start: 0.7918 (m-30) cc_final: 0.7569 (m-30) REVERT: A 366 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7997 (mt-10) REVERT: A 547 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7531 (mmmm) REVERT: A 588 LYS cc_start: 0.8422 (mtpp) cc_final: 0.7939 (ptmm) REVERT: A 627 LYS cc_start: 0.8408 (mtmt) cc_final: 0.8018 (pttp) REVERT: A 650 MET cc_start: 0.7231 (mmm) cc_final: 0.6463 (mmp) REVERT: A 680 ASP cc_start: 0.6611 (m-30) cc_final: 0.6196 (m-30) outliers start: 21 outliers final: 8 residues processed: 102 average time/residue: 0.5701 time to fit residues: 61.8675 Evaluate side-chains 93 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 526 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [56, 30, 25, 53, 60, 59, 28, 1, 27, 80, 49] chunk 56 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.0050 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN ** A 509 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 = 0.4022 r_free = 0.4022 target = 0.164852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131996 restraints weight = 10094.231| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.57 r_work: 0.3409 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8549 Z= 0.135 Angle : 0.521 7.137 11932 Z= 0.297 Chirality : 0.039 0.177 1350 Planarity : 0.003 0.037 1167 Dihedral : 20.909 94.595 2181 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.76 % Allowed : 16.57 % Favored : 80.67 % 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: 0.32 (0.31), residues: 736 helix: 1.05 (0.27), residues: 363 sheet: -0.32 (0.56), residues: 76 loop : -0.60 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 141 TYR 0.024 0.002 TYR A 437 PHE 0.020 0.001 PHE A 603 TRP 0.009 0.001 TRP A 172 HIS 0.002 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 ( 8544) covalent geometry : angle 0.52072 / 0.30 (11932) hydrogen bonds : bond 0.04760 / 3.18 ( 357) hydrogen bonds : angle 3.95206 / 2.74 ( 957) Misc. bond : bond 0.00081 / 0.05 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7727 (mp) REVERT: A 206 MET cc_start: 0.6770 (tpp) cc_final: 0.6393 (tpp) REVERT: A 210 LYS cc_start: 0.7815 (ttmt) cc_final: 0.7501 (mtmt) REVERT: A 273 VAL cc_start: 0.7878 (t) cc_final: 0.7629 (m) REVERT: A 326 ASN cc_start: 0.7752 (m-40) cc_final: 0.7280 (m110) REVERT: A 356 ASP cc_start: 0.7914 (m-30) cc_final: 0.7491 (m-30) REVERT: A 360 ASN cc_start: 0.8481 (m-40) cc_final: 0.8253 (m-40) REVERT: A 547 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7532 (mmmm) REVERT: A 588 LYS cc_start: 0.8457 (mtpp) cc_final: 0.7968 (ptmm) REVERT: A 627 LYS cc_start: 0.8404 (mtmt) cc_final: 0.8029 (pttp) REVERT: A 650 MET cc_start: 0.7241 (mmm) cc_final: 0.6522 (mmp) REVERT: A 680 ASP cc_start: 0.6612 (m-30) cc_final: 0.6243 (m-30) outliers start: 19 outliers final: 8 residues processed: 103 average time/residue: 0.5986 time to fit residues: 65.4498 Evaluate side-chains 91 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 734 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [19, 69, 43, 68, 61, 45, 76, 77, 11, 41, 23] chunk 19 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 509 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 = 0.4025 r_free = 0.4025 target = 0.164879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.132735 restraints weight = 10183.538| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.57 r_work: 0.3426 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8549 Z= 0.141 Angle : 0.527 6.964 11932 Z= 0.299 Chirality : 0.039 0.174 1350 Planarity : 0.003 0.037 1167 Dihedral : 20.721 95.040 2181 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.76 % Allowed : 16.42 % Favored : 80.81 % 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: 0.40 (0.31), residues: 736 helix: 1.13 (0.28), residues: 361 sheet: -0.38 (0.57), residues: 76 loop : -0.55 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 141 TYR 0.024 0.002 TYR A 437 PHE 0.020 0.001 PHE A 603 TRP 0.010 0.002 TRP A 172 HIS 0.003 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 8544) covalent geometry : angle 0.52687 / 0.30 (11932) hydrogen bonds : bond 0.04722 / 3.16 ( 357) hydrogen bonds : angle 3.91718 / 2.72 ( 957) Misc. bond : bond 0.00071 / 0.04 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7775 (mp) REVERT: A 198 LYS cc_start: 0.7558 (pptt) cc_final: 0.7284 (pptt) REVERT: A 206 MET cc_start: 0.6745 (tpp) cc_final: 0.6329 (tpp) REVERT: A 210 LYS cc_start: 0.7840 (ttmt) cc_final: 0.7522 (mtmt) REVERT: A 273 VAL cc_start: 0.7711 (OUTLIER) cc_final: 0.7351 (m) REVERT: A 326 ASN cc_start: 0.7753 (m-40) cc_final: 0.7505 (m110) REVERT: A 356 ASP cc_start: 0.7885 (m-30) cc_final: 0.7445 (m-30) REVERT: A 360 ASN cc_start: 0.8494 (m-40) cc_final: 0.8261 (m-40) REVERT: A 547 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7558 (mmmm) REVERT: A 588 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8005 (ptmm) REVERT: A 627 LYS cc_start: 0.8309 (mtmt) cc_final: 0.7991 (pttp) REVERT: A 680 ASP cc_start: 0.6587 (m-30) cc_final: 0.6245 (m-30) outliers start: 19 outliers final: 9 residues processed: 100 average time/residue: 0.5227 time to fit residues: 55.7681 Evaluate side-chains 92 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 734 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [1, 25, 17, 37, 60, 46, 56, 19, 53, 9, 59] chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.162691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.130307 restraints weight = 10175.725| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.56 r_work: 0.3389 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8549 Z= 0.202 Angle : 0.570 5.881 11932 Z= 0.319 Chirality : 0.042 0.180 1350 Planarity : 0.003 0.038 1167 Dihedral : 20.663 95.229 2181 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.49 % Allowed : 17.01 % Favored : 79.51 % 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: 0.18 (0.31), residues: 736 helix: 0.91 (0.27), residues: 363 sheet: -0.42 (0.58), residues: 77 loop : -0.64 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 141 TYR 0.027 0.002 TYR A 437 PHE 0.021 0.002 PHE A 603 TRP 0.015 0.002 TRP A 172 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 ( 8544) covalent geometry : angle 0.56988 / 0.32 (11932) hydrogen bonds : bond 0.05273 / 3.51 ( 357) hydrogen bonds : angle 4.06942 / 2.82 ( 957) Misc. bond : bond 0.00081 / 0.04 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7878 (mp) REVERT: A 206 MET cc_start: 0.6939 (tpp) cc_final: 0.6480 (tpp) REVERT: A 210 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7496 (mtmt) REVERT: A 273 VAL cc_start: 0.7745 (OUTLIER) cc_final: 0.7422 (m) REVERT: A 356 ASP cc_start: 0.7966 (m-30) cc_final: 0.7515 (m-30) REVERT: A 360 ASN cc_start: 0.8500 (m-40) cc_final: 0.8256 (m-40) REVERT: A 547 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7520 (mmmm) REVERT: A 588 LYS cc_start: 0.8487 (mtpp) cc_final: 0.7957 (ptmm) REVERT: A 627 LYS cc_start: 0.8336 (mtmt) cc_final: 0.8017 (pttp) REVERT: A 641 MET cc_start: 0.8085 (mtp) cc_final: 0.7878 (mtm) REVERT: A 680 ASP cc_start: 0.6654 (m-30) cc_final: 0.6352 (m-30) outliers start: 24 outliers final: 13 residues processed: 99 average time/residue: 0.5236 time to fit residues: 55.3106 Evaluate side-chains 95 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 734 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [32, 27, 49, 22, 48, 39, 62, 46, 41, 37, 26] chunk 32 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN ** A 509 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 = 0.4051 r_free = 0.4051 target = 0.167291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.135429 restraints weight = 10139.488| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.55 r_work: 0.3465 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8549 Z= 0.119 Angle : 0.524 7.934 11932 Z= 0.299 Chirality : 0.038 0.167 1350 Planarity : 0.003 0.038 1167 Dihedral : 20.519 95.959 2181 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.18 % Allowed : 18.02 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.31), residues: 736 helix: 1.10 (0.28), residues: 364 sheet: -0.27 (0.59), residues: 76 loop : -0.51 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 197 TYR 0.024 0.002 TYR A 437 PHE 0.018 0.001 PHE A 603 TRP 0.008 0.002 TRP A 172 HIS 0.005 0.001 HIS A 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 ( 8544) covalent geometry : angle 0.52416 / 0.30 (11932) hydrogen bonds : bond 0.04488 / 3.02 ( 357) hydrogen bonds : angle 3.90704 / 2.72 ( 957) Misc. bond : bond 0.00055 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7986 (mp) REVERT: A 199 CYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7229 (t) REVERT: A 206 MET cc_start: 0.6890 (tpp) cc_final: 0.6490 (tpp) REVERT: A 210 LYS cc_start: 0.7733 (ttmt) cc_final: 0.7434 (mtmt) REVERT: A 326 ASN cc_start: 0.7740 (m-40) cc_final: 0.7496 (m110) REVERT: A 356 ASP cc_start: 0.7908 (m-30) cc_final: 0.7431 (m-30) REVERT: A 360 ASN cc_start: 0.8527 (m-40) cc_final: 0.8289 (m-40) REVERT: A 588 LYS cc_start: 0.8457 (mtpp) cc_final: 0.7951 (ptmm) REVERT: A 627 LYS cc_start: 0.8291 (mtmt) cc_final: 0.8056 (pttp) REVERT: A 680 ASP cc_start: 0.6658 (m-30) cc_final: 0.6312 (m-30) outliers start: 15 outliers final: 7 residues processed: 94 average time/residue: 0.5410 time to fit residues: 54.2420 Evaluate side-chains 92 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 526 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [80, 12, 42, 2, 29, 73, 3, 25, 52, 60, 45] chunk 80 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN ** A 509 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 = 0.4040 r_free = 0.4040 target = 0.166353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.134526 restraints weight = 10082.019| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.53 r_work: 0.3456 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8549 Z= 0.146 Angle : 0.560 9.403 11932 Z= 0.313 Chirality : 0.039 0.179 1350 Planarity : 0.003 0.039 1167 Dihedral : 20.443 96.235 2181 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.03 % Allowed : 18.60 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.31), residues: 736 helix: 1.10 (0.27), residues: 362 sheet: -0.32 (0.58), residues: 76 loop : -0.56 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 197 TYR 0.024 0.002 TYR A 437 PHE 0.018 0.001 PHE A 603 TRP 0.007 0.002 TRP A 33 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 ( 8544) covalent geometry : angle 0.56041 / 0.31 (11932) hydrogen bonds : bond 0.04613 / 3.08 ( 357) hydrogen bonds : angle 3.91128 / 2.71 ( 957) Misc. bond : bond 0.00056 / 0.03 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8076 (tptp) cc_final: 0.7801 (tptp) REVERT: A 54 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.8008 (mp) REVERT: A 197 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7022 (ttm-80) REVERT: A 206 MET cc_start: 0.6846 (tpp) cc_final: 0.6378 (tpt) REVERT: A 273 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7473 (m) REVERT: A 356 ASP cc_start: 0.7975 (m-30) cc_final: 0.7490 (m-30) REVERT: A 360 ASN cc_start: 0.8515 (m-40) cc_final: 0.8272 (m-40) REVERT: A 588 LYS cc_start: 0.8456 (mtpp) cc_final: 0.7948 (ptmm) REVERT: A 627 LYS cc_start: 0.8309 (mtmt) cc_final: 0.8075 (pttp) REVERT: A 680 ASP cc_start: 0.6665 (m-30) cc_final: 0.6416 (m-30) outliers start: 14 outliers final: 7 residues processed: 93 average time/residue: 0.5431 time to fit residues: 53.8737 Evaluate side-chains 91 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: [2, 1, 42, 49, 59, 33, 17, 6, 24, 18, 38] chunk 2 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 ASN ** A 509 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 = 0.4032 r_free = 0.4032 target = 0.165679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133546 restraints weight = 10131.915| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.54 r_work: 0.3437 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8549 Z= 0.147 Angle : 0.557 11.969 11932 Z= 0.312 Chirality : 0.039 0.166 1350 Planarity : 0.003 0.039 1167 Dihedral : 20.412 96.529 2181 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.18 % Allowed : 19.19 % Favored : 78.63 % 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: 0.34 (0.31), residues: 736 helix: 1.00 (0.27), residues: 366 sheet: -0.35 (0.58), residues: 76 loop : -0.49 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 133 TYR 0.024 0.002 TYR A 437 PHE 0.019 0.001 PHE A 603 TRP 0.007 0.002 TRP A 33 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 ( 8544) covalent geometry : angle 0.55742 / 0.31 (11932) hydrogen bonds : bond 0.04681 / 3.12 ( 357) hydrogen bonds : angle 3.98550 / 2.76 ( 957) Misc. bond : bond 0.00051 / 0.03 ( 5) =============================================================================== Job complete usr+sys time: 2784.42 seconds wall clock time: 48 minutes 10.58 seconds (2890.58 seconds total)