Starting phenix.real_space_refine on Fri Jul 3 01:48:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7way_32389/07_2026/7way_32389.cif Found real_map, /net/cci-nas-00/data/ceres_data/7way_32389/07_2026/7way_32389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7way_32389/07_2026/7way_32389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7way_32389/07_2026/7way_32389.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7way_32389/07_2026/7way_32389.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7way_32389/07_2026/7way_32389.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7way_32389/07_2026/7way_32389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7way_32389/07_2026/7way_32389.map" } resolution = 2.9 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 175 5.49 5 S 28 5.16 5 C 6630 2.51 5 N 2041 2.21 5 O 2579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11453 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 674 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "C" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 547 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "D" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2446 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 55, 'rna3p_pyr': 48} Link IDs: {'rna2p': 12, 'rna3p': 102} Chain breaks: 1 Chain: "A" Number of atoms: 7786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 7786 Classifications: {'peptide': 960} Link IDs: {'PTRANS': 37, 'TRANS': 922} Chain breaks: 2 Time building chain proxies: 2.13, per 1000 atoms: 0.19 Number of scatterers: 11453 At special positions: 0 Unit cell: (100.58, 141.94, 125.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 175 15.00 O 2579 8.00 N 2041 7.00 C 6630 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: 0.83 Conformation dependent library (CDL) restraints added in 415.2 milliseconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 49.6% alpha, 22.4% beta 61 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 60 through 92 Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 221 through 272 removed outlier: 3.644A pdb=" N VAL A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 309 Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.689A pdb=" N LYS A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 371 through 378 removed outlier: 4.135A pdb=" N GLN A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 394 through 411 Processing helix chain 'A' and resid 413 through 443 removed outlier: 3.532A pdb=" N VAL A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 466 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 472 through 493 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 510 through 513 Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 697 through 717 Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 725 through 750 Processing helix chain 'A' and resid 770 through 774 Processing helix chain 'A' and resid 775 through 790 removed outlier: 3.550A pdb=" N MET A 779 " --> pdb=" O GLN A 775 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 796 Processing helix chain 'A' and resid 818 through 829 Processing helix chain 'A' and resid 866 through 876 removed outlier: 3.981A pdb=" N GLU A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 885 Processing helix chain 'A' and resid 886 through 901 Processing helix chain 'A' and resid 921 through 936 removed outlier: 3.594A pdb=" N ALA A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 949 removed outlier: 3.518A pdb=" N THR A 949 " --> pdb=" O GLN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 973 removed outlier: 3.887A pdb=" N PHE A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 502 through 506 removed outlier: 3.643A pdb=" N GLY A 614 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR A 638 " --> pdb=" O ALA A 612 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY A 614 " --> pdb=" O ALA A 636 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA A 636 " --> pdb=" O GLY A 614 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL A 616 " --> pdb=" O PHE A 634 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE A 634 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU A 618 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA A 632 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR A 620 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU A 630 " --> pdb=" O THR A 620 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR A 622 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN A 628 " --> pdb=" O TYR A 622 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 633 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 502 through 506 removed outlier: 3.643A pdb=" N GLY A 614 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR A 638 " --> pdb=" O ALA A 612 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY A 614 " --> pdb=" O ALA A 636 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA A 636 " --> pdb=" O GLY A 614 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL A 616 " --> pdb=" O PHE A 634 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE A 634 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU A 618 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA A 632 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR A 620 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU A 630 " --> pdb=" O THR A 620 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR A 622 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN A 628 " --> pdb=" O TYR A 622 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 633 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 13.056A pdb=" N CYS A 515 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N ASN A 561 " --> pdb=" O CYS A 515 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE A 517 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL A 559 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE A 556 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 117 removed outlier: 4.365A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL A 139 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 128 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL A 139 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N SER A 126 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 114 through 117 removed outlier: 4.365A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL A 139 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N THR A 153 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR A 155 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 691 through 694 removed outlier: 4.520A pdb=" N ALA A 756 " --> pdb=" O ILE A 658 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ARG A 660 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 Processing sheet with id=AA8, first strand: chain 'A' and resid 830 through 832 removed outlier: 3.747A pdb=" N THR A 838 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 850 through 855 Processing sheet with id=AB1, first strand: chain 'A' and resid 909 through 911 447 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 151 hydrogen bonds 290 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 1.12 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: 2340 1.33 - 1.45: 3480 1.45 - 1.57: 5834 1.57 - 1.69: 346 1.69 - 1.81: 41 Bond restraints: 12041 Sorted by residual: bond pdb=" C3' DT B 2 " pdb=" C2' DT B 2 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.61e+00 bond pdb=" C3' DC C 24 " pdb=" C2' DC C 24 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.59e+00 bond pdb=" C3' DA B 24 " pdb=" C2' DA B 24 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.71e+00 bond pdb=" C3' DT B 3 " pdb=" C2' DT B 3 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.31e+00 bond pdb=" C1' DC C 19 " pdb=" N1 DC C 19 " ideal model delta sigma weight residual 1.468 1.502 -0.034 1.40e-02 5.10e+03 5.96e+00 ... (remaining 12036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 16783 2.10 - 4.20: 238 4.20 - 6.30: 12 6.30 - 8.40: 4 8.40 - 10.50: 1 Bond angle restraints: 17038 Sorted by residual: angle pdb=" N3 DT B 8 " pdb=" C4 DT B 8 " pdb=" O4 DT B 8 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT B 2 " pdb=" C4 DT B 2 " pdb=" O4 DT B 2 " 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 21 " pdb=" C4 DT C 21 " pdb=" O4 DT C 21 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT B 14 " pdb=" C4 DT B 14 " pdb=" O4 DT B 14 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT B 11 " pdb=" C4 DT B 11 " pdb=" O4 DT B 11 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 17033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.00: 6475 32.00 - 64.00: 397 64.00 - 96.01: 17 96.01 - 128.01: 0 128.01 - 160.01: 2 Dihedral angle restraints: 6891 sinusoidal: 4089 harmonic: 2802 Sorted by residual: dihedral pdb=" O4' U D 17 " pdb=" C1' U D 17 " pdb=" N1 U D 17 " pdb=" C2 U D 17 " ideal model delta sinusoidal sigma weight residual 232.00 90.82 141.18 1 1.70e+01 3.46e-03 5.91e+01 dihedral pdb=" CA ARG A 443 " pdb=" C ARG A 443 " pdb=" N SER A 444 " pdb=" CA SER A 444 " ideal model delta harmonic sigma weight residual -180.00 -154.38 -25.62 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA LEU A 527 " pdb=" C LEU A 527 " pdb=" N ASN A 528 " pdb=" CA ASN A 528 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 6888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1712 0.057 - 0.115: 225 0.115 - 0.172: 23 0.172 - 0.229: 0 0.229 - 0.286: 1 Chirality restraints: 1961 Sorted by residual: chirality pdb=" CG LEU A 529 " pdb=" CB LEU A 529 " pdb=" CD1 LEU A 529 " pdb=" CD2 LEU A 529 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C3' C D 40 " pdb=" C4' C D 40 " pdb=" O3' C D 40 " pdb=" C2' C D 40 " both_signs ideal model delta sigma weight residual False -2.48 -2.33 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" C1' C D 19 " pdb=" O4' C D 19 " pdb=" C2' C D 19 " pdb=" N1 C D 19 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1958 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 56 " -0.024 2.00e-02 2.50e+03 1.08e-02 3.18e+00 pdb=" N9 A D 56 " 0.024 2.00e-02 2.50e+03 pdb=" C8 A D 56 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A D 56 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A D 56 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A D 56 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A D 56 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A D 56 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 56 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A D 56 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A D 56 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 38 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 39 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 529 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C LEU A 529 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU A 529 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR A 530 " -0.009 2.00e-02 2.50e+03 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 592 2.72 - 3.26: 10071 3.26 - 3.81: 19637 3.81 - 4.35: 24195 4.35 - 4.90: 37246 Nonbonded interactions: 91741 Sorted by model distance: nonbonded pdb=" OG1 THR A 816 " pdb=" NE2 GLN A 963 " model vdw 2.172 3.120 nonbonded pdb=" OG1 THR A 38 " pdb=" OD1 ASP A 40 " model vdw 2.190 3.040 nonbonded pdb=" O2' C D 40 " pdb=" OP1 U D 41 " model vdw 2.209 3.040 nonbonded pdb=" O HIS A 173 " pdb=" OG1 THR A 183 " model vdw 2.224 3.040 nonbonded pdb=" OD1 ASP A 865 " pdb=" OG SER A 867 " model vdw 2.233 3.040 ... (remaining 91736 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: 1.250 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.930 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:8.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 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 : 0.004 0.038 12041 Z= 0.289 Angle : 0.589 10.496 17038 Z= 0.411 Chirality : 0.038 0.286 1961 Planarity : 0.004 0.043 1543 Dihedral : 16.755 160.010 5081 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 1.31 (0.28), residues: 954 helix: 2.23 (0.25), residues: 430 sheet: -0.08 (0.43), residues: 139 loop : -0.28 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 956 TYR 0.019 0.001 TYR A 776 PHE 0.008 0.001 PHE A 543 TRP 0.012 0.001 TRP A 519 HIS 0.005 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.29 (12041) covalent geometry : angle 0.58856 / 0.41 (17038) hydrogen bonds : bond 0.11559 / 12.32 ( 571) hydrogen bonds : angle 4.76739 / 6.62 ( 1556) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.336 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 54 average time/residue: 0.6510 time to fit residues: 37.7928 Evaluate side-chains 35 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN A 907 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.111056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.075796 restraints weight = 22388.589| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.53 r_work: 0.2776 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.0612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12041 Z= 0.232 Angle : 0.598 6.866 17038 Z= 0.328 Chirality : 0.041 0.216 1961 Planarity : 0.004 0.045 1543 Dihedral : 18.181 165.441 3073 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.72 % Allowed : 4.89 % Favored : 94.40 % 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: 1.30 (0.28), residues: 954 helix: 2.19 (0.25), residues: 438 sheet: -0.13 (0.43), residues: 139 loop : -0.29 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 764 TYR 0.022 0.002 TYR A 372 PHE 0.012 0.002 PHE A 517 TRP 0.014 0.002 TRP A 86 HIS 0.010 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (12041) covalent geometry : angle 0.59770 / 0.33 (17038) hydrogen bonds : bond 0.06572 / 7.26 ( 571) hydrogen bonds : angle 4.10870 / 5.72 ( 1556) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.280 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 38 average time/residue: 0.5936 time to fit residues: 24.3700 Evaluate side-chains 35 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 12 optimal weight: 40.0000 chunk 74 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.111797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.076484 restraints weight = 22610.732| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.60 r_work: 0.2789 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12041 Z= 0.165 Angle : 0.541 6.731 17038 Z= 0.301 Chirality : 0.038 0.173 1961 Planarity : 0.004 0.044 1543 Dihedral : 18.214 164.538 3073 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.83 % Allowed : 5.72 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.28), residues: 954 helix: 2.24 (0.25), residues: 440 sheet: -0.11 (0.43), residues: 139 loop : -0.29 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 824 TYR 0.016 0.001 TYR A 85 PHE 0.009 0.001 PHE A 517 TRP 0.012 0.001 TRP A 598 HIS 0.007 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (12041) covalent geometry : angle 0.54080 / 0.30 (17038) hydrogen bonds : bond 0.05867 / 6.48 ( 571) hydrogen bonds : angle 3.94265 / 5.47 ( 1556) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.336 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.6038 time to fit residues: 26.7686 Evaluate side-chains 36 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 95 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 GLN A 340 ASN A 368 ASN A 737 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.111841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.076709 restraints weight = 22512.625| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.44 r_work: 0.2797 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12041 Z= 0.161 Angle : 0.532 8.538 17038 Z= 0.295 Chirality : 0.038 0.253 1961 Planarity : 0.004 0.043 1543 Dihedral : 18.211 163.212 3073 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.72 % Allowed : 7.15 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.28), residues: 954 helix: 2.30 (0.25), residues: 441 sheet: -0.10 (0.43), residues: 139 loop : -0.28 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 824 TYR 0.023 0.002 TYR A 372 PHE 0.013 0.001 PHE A 196 TRP 0.013 0.001 TRP A 86 HIS 0.007 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (12041) covalent geometry : angle 0.53229 / 0.29 (17038) hydrogen bonds : bond 0.05611 / 6.20 ( 571) hydrogen bonds : angle 3.85161 / 5.35 ( 1556) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.265 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 0.6147 time to fit residues: 28.9037 Evaluate side-chains 41 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 17 optimal weight: 0.0870 chunk 45 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 63 optimal weight: 0.2980 overall best weight: 2.8764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.110717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.075181 restraints weight = 22367.087| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.48 r_work: 0.2767 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12041 Z= 0.215 Angle : 0.577 7.484 17038 Z= 0.316 Chirality : 0.040 0.215 1961 Planarity : 0.004 0.043 1543 Dihedral : 18.215 161.097 3073 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.83 % Allowed : 9.06 % Favored : 90.11 % 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: 1.34 (0.28), residues: 954 helix: 2.23 (0.25), residues: 442 sheet: -0.12 (0.44), residues: 137 loop : -0.30 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 824 TYR 0.021 0.002 TYR A 776 PHE 0.011 0.002 PHE A 463 TRP 0.014 0.002 TRP A 86 HIS 0.010 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.22 (12041) covalent geometry : angle 0.57683 / 0.32 (17038) hydrogen bonds : bond 0.06308 / 6.97 ( 571) hydrogen bonds : angle 3.91807 / 5.45 ( 1556) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.333 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.5533 time to fit residues: 24.6744 Evaluate side-chains 40 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 0.0970 chunk 111 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 99 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.113218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.078080 restraints weight = 22656.915| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.40 r_work: 0.2839 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12041 Z= 0.115 Angle : 0.509 9.106 17038 Z= 0.282 Chirality : 0.036 0.175 1961 Planarity : 0.004 0.042 1543 Dihedral : 18.133 157.677 3073 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.60 % Allowed : 10.13 % Favored : 89.27 % 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: 1.53 (0.28), residues: 954 helix: 2.42 (0.25), residues: 443 sheet: -0.07 (0.43), residues: 138 loop : -0.25 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 824 TYR 0.025 0.001 TYR A 372 PHE 0.008 0.001 PHE A 196 TRP 0.012 0.001 TRP A 598 HIS 0.002 0.001 HIS A 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.11 (12041) covalent geometry : angle 0.50933 / 0.28 (17038) hydrogen bonds : bond 0.04882 / 5.43 ( 571) hydrogen bonds : angle 3.72135 / 5.11 ( 1556) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.307 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 0.5635 time to fit residues: 25.7886 Evaluate side-chains 42 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 0.1980 chunk 84 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.112095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.076951 restraints weight = 22558.322| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.58 r_work: 0.2802 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12041 Z= 0.150 Angle : 0.535 15.756 17038 Z= 0.290 Chirality : 0.037 0.183 1961 Planarity : 0.004 0.041 1543 Dihedral : 18.210 156.825 3073 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.83 % Allowed : 10.49 % Favored : 88.68 % 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: 1.55 (0.28), residues: 954 helix: 2.42 (0.25), residues: 443 sheet: -0.00 (0.44), residues: 136 loop : -0.23 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 956 TYR 0.016 0.001 TYR A 85 PHE 0.009 0.001 PHE A 196 TRP 0.012 0.001 TRP A 86 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (12041) covalent geometry : angle 0.53478 / 0.29 (17038) hydrogen bonds : bond 0.05254 / 5.81 ( 571) hydrogen bonds : angle 3.76310 / 5.17 ( 1556) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.321 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 0.5558 time to fit residues: 26.7020 Evaluate side-chains 40 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.110437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.075248 restraints weight = 22319.307| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.53 r_work: 0.2761 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12041 Z= 0.211 Angle : 0.593 16.215 17038 Z= 0.317 Chirality : 0.039 0.190 1961 Planarity : 0.004 0.041 1543 Dihedral : 18.093 156.036 3073 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.07 % Allowed : 10.25 % Favored : 88.68 % 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: 1.49 (0.28), residues: 954 helix: 2.46 (0.25), residues: 435 sheet: -0.09 (0.44), residues: 137 loop : -0.31 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 956 TYR 0.025 0.002 TYR A 372 PHE 0.016 0.002 PHE A 196 TRP 0.015 0.002 TRP A 86 HIS 0.007 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (12041) covalent geometry : angle 0.59267 / 0.32 (17038) hydrogen bonds : bond 0.06189 / 6.84 ( 571) hydrogen bonds : angle 3.88786 / 5.38 ( 1556) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.286 Fit side-chains REVERT: A 486 TRP cc_start: 0.8091 (m-10) cc_final: 0.7797 (m-10) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.6197 time to fit residues: 29.6198 Evaluate side-chains 45 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 93 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.111998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.076957 restraints weight = 22285.339| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.40 r_work: 0.2804 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12041 Z= 0.127 Angle : 0.562 16.676 17038 Z= 0.300 Chirality : 0.037 0.185 1961 Planarity : 0.004 0.090 1543 Dihedral : 18.250 155.475 3073 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.60 % Allowed : 10.97 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.28), residues: 954 helix: 2.51 (0.25), residues: 435 sheet: -0.01 (0.44), residues: 136 loop : -0.27 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 824 TYR 0.014 0.001 TYR A 244 PHE 0.013 0.001 PHE A 196 TRP 0.013 0.001 TRP A 782 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.13 (12041) covalent geometry : angle 0.56186 / 0.30 (17038) hydrogen bonds : bond 0.05305 / 5.86 ( 571) hydrogen bonds : angle 3.78751 / 5.21 ( 1556) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.346 Fit side-chains REVERT: A 195 ASP cc_start: 0.8289 (t70) cc_final: 0.8068 (t70) REVERT: A 292 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8306 (tt0) outliers start: 5 outliers final: 6 residues processed: 44 average time/residue: 0.6015 time to fit residues: 28.8891 Evaluate side-chains 45 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 82 optimal weight: 0.0370 chunk 95 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.112178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.076995 restraints weight = 22391.448| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.40 r_work: 0.2811 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12041 Z= 0.138 Angle : 0.552 16.561 17038 Z= 0.295 Chirality : 0.037 0.186 1961 Planarity : 0.004 0.042 1543 Dihedral : 18.191 155.402 3073 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.83 % Allowed : 10.85 % Favored : 88.32 % 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: 1.61 (0.28), residues: 954 helix: 2.54 (0.25), residues: 436 sheet: -0.12 (0.42), residues: 153 loop : -0.17 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 824 TYR 0.024 0.001 TYR A 372 PHE 0.010 0.001 PHE A 196 TRP 0.013 0.001 TRP A 86 HIS 0.002 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (12041) covalent geometry : angle 0.55195 / 0.30 (17038) hydrogen bonds : bond 0.05191 / 5.73 ( 571) hydrogen bonds : angle 3.74697 / 5.14 ( 1556) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.336 Fit side-chains REVERT: A 195 ASP cc_start: 0.8254 (t70) cc_final: 0.8039 (t70) REVERT: A 486 TRP cc_start: 0.8067 (m-10) cc_final: 0.7759 (m-10) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 0.6390 time to fit residues: 31.2940 Evaluate side-chains 44 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 780 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 103 optimal weight: 0.0980 chunk 10 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.112618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.077474 restraints weight = 22497.111| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.54 r_work: 0.2819 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12041 Z= 0.127 Angle : 0.546 16.234 17038 Z= 0.292 Chirality : 0.037 0.186 1961 Planarity : 0.004 0.040 1543 Dihedral : 18.255 155.091 3073 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.60 % Allowed : 10.73 % Favored : 88.68 % 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: 1.61 (0.28), residues: 954 helix: 2.52 (0.25), residues: 436 sheet: -0.09 (0.42), residues: 153 loop : -0.16 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 824 TYR 0.015 0.001 TYR A 85 PHE 0.011 0.001 PHE A 196 TRP 0.012 0.001 TRP A 782 HIS 0.002 0.001 HIS A 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (12041) covalent geometry : angle 0.54606 / 0.29 (17038) hydrogen bonds : bond 0.04975 / 5.50 ( 571) hydrogen bonds : angle 3.71720 / 5.08 ( 1556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2954.35 seconds wall clock time: 51 minutes 18.07 seconds (3078.07 seconds total)