Starting phenix.real_space_refine on Fri Sep 11 21:00:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wb1_32392/09_2026/7wb1_32392.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wb1_32392/09_2026/7wb1_32392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wb1_32392/09_2026/7wb1_32392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wb1_32392/09_2026/7wb1_32392.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wb1_32392/09_2026/7wb1_32392.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wb1_32392/09_2026/7wb1_32392.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wb1_32392/09_2026/7wb1_32392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wb1_32392/09_2026/7wb1_32392.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 178 5.49 5 S 28 5.16 5 C 6661 2.51 5 N 2059 2.21 5 O 2598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11524 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 614 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} 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: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2577 Classifications: {'RNAv2': 121} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 59, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 106} 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: 2.81, per 1000 atoms: 0.24 Number of scatterers: 11524 At special positions: 0 Unit cell: (101.52, 141, 121.26, 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 178 15.00 O 2598 8.00 N 2059 7.00 C 6661 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: 1.01 Conformation dependent library (CDL) restraints added in 418.0 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: 35 helices and 12 sheets defined 49.4% alpha, 13.1% beta 62 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 1.47 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 removed outlier: 3.735A pdb=" N ARG A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 195 through 201 removed outlier: 3.552A pdb=" N ILE A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 222 through 271 removed outlier: 3.577A pdb=" N ASP A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 309 Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.605A pdb=" N GLU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 removed outlier: 3.748A pdb=" N GLY A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 378 removed outlier: 3.755A 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 removed outlier: 3.807A pdb=" N LYS A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 411 Processing helix chain 'A' and resid 413 through 443 removed outlier: 4.041A pdb=" N VAL A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR A 418 " --> pdb=" O TRP A 414 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASP A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 466 removed outlier: 4.200A pdb=" N LYS A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) 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 589 through 596 Processing helix chain 'A' and resid 697 through 717 removed outlier: 3.602A pdb=" N LYS A 701 " --> pdb=" O SER A 697 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 715 " --> pdb=" O VAL A 711 " (cutoff:3.500A) 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 776 through 789 Processing helix chain 'A' and resid 793 through 798 removed outlier: 4.163A pdb=" N TYR A 797 " --> pdb=" O PRO A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 829 removed outlier: 3.504A pdb=" N LYS A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 874 Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 881 through 885 Processing helix chain 'A' and resid 886 through 901 removed outlier: 3.754A pdb=" N GLU A 892 " --> pdb=" O GLY A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 937 removed outlier: 3.835A pdb=" N GLN A 924 " --> pdb=" O HIS A 920 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A 937 " --> pdb=" O TRP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 949 Processing helix chain 'A' and resid 954 through 971 removed outlier: 3.805A 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: 3.505A pdb=" N SER A 502 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 614 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU A 611 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU A 640 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN A 613 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 633 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 36 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 35 " --> pdb=" O ALA A 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 removed outlier: 4.525A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 135 " --> pdb=" O CYS A 130 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A 128 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 115 removed outlier: 4.525A pdb=" N ILE A 114 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A 155 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 145 removed outlier: 3.629A pdb=" N GLN A 144 " --> pdb=" O HIS A 152 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 152 " --> pdb=" O GLN A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 542 through 545 removed outlier: 3.504A pdb=" N ARG A 542 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 573 " --> pdb=" O ARG A 542 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 572 " --> pdb=" O PHE A 556 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A 556 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL A 559 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N PHE A 517 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N ASN A 561 " --> pdb=" O CYS A 515 " (cutoff:3.500A) removed outlier: 12.651A pdb=" N CYS A 515 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 622 through 623 Processing sheet with id=AA8, first strand: chain 'A' and resid 691 through 694 removed outlier: 4.777A pdb=" N ALA A 756 " --> pdb=" O ILE A 658 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR A 801 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE A 755 " --> pdb=" O THR A 801 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 682 Processing sheet with id=AB1, first strand: chain 'A' and resid 830 through 831 removed outlier: 3.513A pdb=" N LYS A 830 " --> pdb=" O MET A 837 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 850 through 853 removed outlier: 4.192A pdb=" N TYR A 853 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL A 862 " --> pdb=" O TYR A 853 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 910 through 911 382 hydrogen bonds defined for protein. 1095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 150 hydrogen bonds 276 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 1.36 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: 2385 1.33 - 1.45: 3515 1.45 - 1.57: 5830 1.57 - 1.69: 353 1.69 - 1.81: 41 Bond restraints: 12124 Sorted by residual: bond pdb=" C3' DT C 14 " pdb=" C2' DT C 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DG B 19 " pdb=" C2' DG B 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.65e+00 bond pdb=" C3' DC C 23 " pdb=" C2' DC C 23 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.67e+00 bond pdb=" C3' DC C 25 " pdb=" C2' DC C 25 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.52e+00 bond pdb=" C3' DG B 4 " pdb=" C2' DG B 4 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.93e+00 ... (remaining 12119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 15976 1.32 - 2.64: 872 2.64 - 3.96: 267 3.96 - 5.28: 45 5.28 - 6.60: 11 Bond angle restraints: 17171 Sorted by residual: angle pdb=" O4' DT B 8 " pdb=" C4' DT B 8 " pdb=" C3' DT B 8 " ideal model delta sigma weight residual 106.00 103.34 2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT B 14 " pdb=" C4 DT B 14 " pdb=" O4 DT B 14 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT B 11 " pdb=" C4 DT B 11 " pdb=" O4 DT B 11 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT B 8 " pdb=" C4 DT B 8 " pdb=" O4 DT B 8 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" O4' DT C 8 " pdb=" C4' DT C 8 " pdb=" C3' DT C 8 " ideal model delta sigma weight residual 106.00 103.47 2.53 6.00e-01 2.78e+00 1.78e+01 ... (remaining 17166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.23: 6357 34.23 - 68.46: 533 68.46 - 102.69: 37 102.69 - 136.91: 1 136.91 - 171.14: 4 Dihedral angle restraints: 6932 sinusoidal: 4130 harmonic: 2802 Sorted by residual: dihedral pdb=" C4' U D 102 " pdb=" C3' U D 102 " pdb=" C2' U D 102 " pdb=" C1' U D 102 " ideal model delta sinusoidal sigma weight residual 36.34 -36.89 73.23 1 3.10e+00 1.04e-01 7.11e+02 dihedral pdb=" C4' A D 15 " pdb=" C3' A D 15 " pdb=" C2' A D 15 " pdb=" C1' A D 15 " ideal model delta sinusoidal sigma weight residual 36.34 -36.33 72.67 1 3.10e+00 1.04e-01 7.01e+02 dihedral pdb=" C4' C D 12 " pdb=" C3' C D 12 " pdb=" C2' C D 12 " pdb=" C1' C D 12 " ideal model delta sinusoidal sigma weight residual 36.34 -35.91 72.26 1 3.10e+00 1.04e-01 6.95e+02 ... (remaining 6929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1683 0.072 - 0.144: 140 0.144 - 0.216: 25 0.216 - 0.288: 129 0.288 - 0.360: 2 Chirality restraints: 1979 Sorted by residual: chirality pdb=" P A D 95 " pdb=" OP1 A D 95 " pdb=" OP2 A D 95 " pdb=" O5' A D 95 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" P U D 42 " pdb=" OP1 U D 42 " pdb=" OP2 U D 42 " pdb=" O5' U D 42 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' U D 102 " pdb=" C3' U D 102 " pdb=" O2' U D 102 " pdb=" C1' U D 102 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 1976 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C D 104 " 0.009 2.00e-02 2.50e+03 2.56e-02 1.47e+01 pdb=" N1 C D 104 " -0.006 2.00e-02 2.50e+03 pdb=" C2 C D 104 " -0.063 2.00e-02 2.50e+03 pdb=" O2 C D 104 " 0.039 2.00e-02 2.50e+03 pdb=" N3 C D 104 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C D 104 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C D 104 " 0.010 2.00e-02 2.50e+03 pdb=" C5 C D 104 " 0.010 2.00e-02 2.50e+03 pdb=" C6 C D 104 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C D 118 " 0.022 2.00e-02 2.50e+03 1.66e-02 6.17e+00 pdb=" N1 C D 118 " -0.033 2.00e-02 2.50e+03 pdb=" C2 C D 118 " 0.007 2.00e-02 2.50e+03 pdb=" O2 C D 118 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C D 118 " -0.000 2.00e-02 2.50e+03 pdb=" C4 C D 118 " 0.025 2.00e-02 2.50e+03 pdb=" N4 C D 118 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C D 118 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C D 118 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 56 " -0.006 2.00e-02 2.50e+03 1.42e-02 5.57e+00 pdb=" N9 A D 56 " -0.000 2.00e-02 2.50e+03 pdb=" C8 A D 56 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A D 56 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A D 56 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A D 56 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A D 56 " 0.000 2.00e-02 2.50e+03 pdb=" N1 A D 56 " -0.033 2.00e-02 2.50e+03 pdb=" C2 A D 56 " 0.031 2.00e-02 2.50e+03 pdb=" N3 A D 56 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A D 56 " -0.002 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 183 2.62 - 3.19: 9664 3.19 - 3.76: 19864 3.76 - 4.33: 25399 4.33 - 4.90: 38127 Nonbonded interactions: 93237 Sorted by model distance: nonbonded pdb=" N2 G D 59 " pdb=" O2 C D 94 " model vdw 2.046 2.496 nonbonded pdb=" OP2 G D 101 " pdb=" NH2 ARG A 591 " model vdw 2.182 3.120 nonbonded pdb=" NZ LYS A 521 " pdb=" OE2 GLU A 605 " model vdw 2.227 3.120 nonbonded pdb=" O6 DG B 22 " pdb=" NZ LYS A 227 " model vdw 2.236 3.120 nonbonded pdb=" OG1 THR A 202 " pdb=" OE1 GLU A 204 " model vdw 2.263 3.040 ... (remaining 93232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.840 Find NCS groups from input model: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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 0.043 12124 Z= 0.271 Angle : 0.760 6.604 17171 Z= 0.447 Chirality : 0.077 0.360 1979 Planarity : 0.004 0.044 1546 Dihedral : 20.717 171.142 5122 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.72 % Favored : 95.18 % 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: 0.55 (0.28), residues: 954 helix: 1.86 (0.26), residues: 412 sheet: -0.69 (0.45), residues: 140 loop : -0.80 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 764 TYR 0.017 0.001 TYR A 857 PHE 0.016 0.001 PHE A 332 TRP 0.009 0.001 TRP A 962 HIS 0.015 0.002 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.27 (12124) covalent geometry : angle 0.75975 / 0.45 (17171) hydrogen bonds : bond 0.17607 / 19.88 ( 531) hydrogen bonds : angle 5.88496 / 7.55 ( 1371) *********************** 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 84 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.347 Fit side-chains REVERT: A 29 MET cc_start: 0.6905 (ppp) cc_final: 0.5886 (ppp) REVERT: A 375 GLN cc_start: 0.7736 (mm110) cc_final: 0.7534 (tp40) REVERT: A 570 MET cc_start: 0.7668 (tpt) cc_final: 0.7458 (mmm) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1052 time to fit residues: 13.2815 Evaluate side-chains 58 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 HIS A 729 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.093517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.067699 restraints weight = 44144.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.069776 restraints weight = 23813.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.071078 restraints weight = 16744.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.071773 restraints weight = 13720.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.072246 restraints weight = 12350.255| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12124 Z= 0.224 Angle : 1.128 23.741 17171 Z= 0.486 Chirality : 0.100 1.271 1979 Planarity : 0.005 0.048 1546 Dihedral : 21.812 172.754 3112 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.31 % Allowed : 6.91 % Favored : 91.78 % 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: 0.36 (0.28), residues: 954 helix: 1.65 (0.25), residues: 425 sheet: -1.05 (0.43), residues: 144 loop : -0.81 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 624 TYR 0.017 0.002 TYR A 805 PHE 0.021 0.002 PHE A 958 TRP 0.022 0.002 TRP A 366 HIS 0.010 0.002 HIS A 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.22 (12124) covalent geometry : angle 1.12761 / 0.49 (17171) hydrogen bonds : bond 0.07658 / 8.84 ( 531) hydrogen bonds : angle 4.81911 / 6.04 ( 1371) *********************** 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 72 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.361 Fit side-chains REVERT: A 486 TRP cc_start: 0.6993 (m-10) cc_final: 0.6781 (m-10) REVERT: A 570 MET cc_start: 0.8013 (tpt) cc_final: 0.7699 (mmm) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.0903 time to fit residues: 9.2032 Evaluate side-chains 63 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 934 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 GLN A 375 GLN A 520 GLN ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.093455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.067402 restraints weight = 44777.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.069483 restraints weight = 24171.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.070800 restraints weight = 17077.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.071554 restraints weight = 14035.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.071904 restraints weight = 12553.549| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12124 Z= 0.197 Angle : 0.948 13.443 17171 Z= 0.421 Chirality : 0.073 0.608 1979 Planarity : 0.005 0.047 1546 Dihedral : 21.856 171.073 3112 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.67 % Allowed : 9.30 % Favored : 89.03 % 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: 0.36 (0.28), residues: 954 helix: 1.74 (0.25), residues: 419 sheet: -1.14 (0.43), residues: 144 loop : -0.84 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 736 TYR 0.024 0.002 TYR A 698 PHE 0.017 0.002 PHE A 399 TRP 0.013 0.002 TRP A 836 HIS 0.010 0.002 HIS A 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.20 (12124) covalent geometry : angle 0.94849 / 0.42 (17171) hydrogen bonds : bond 0.07462 / 8.97 ( 531) hydrogen bonds : angle 4.56495 / 5.67 ( 1371) *********************** 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 78 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 134 CYS cc_start: 0.8266 (m) cc_final: 0.7690 (t) REVERT: A 231 ASP cc_start: 0.8845 (p0) cc_final: 0.8601 (p0) REVERT: A 570 MET cc_start: 0.7875 (tpt) cc_final: 0.7592 (mmm) outliers start: 14 outliers final: 8 residues processed: 70 average time/residue: 0.0896 time to fit residues: 10.0696 Evaluate side-chains 64 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 934 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 90 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN ** A 561 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 = 0.3919 r_free = 0.3919 target = 0.093904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.067824 restraints weight = 44265.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.069929 restraints weight = 24107.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.071244 restraints weight = 16953.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.072010 restraints weight = 13913.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.072362 restraints weight = 12442.387| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12124 Z= 0.164 Angle : 0.888 12.092 17171 Z= 0.395 Chirality : 0.068 0.473 1979 Planarity : 0.004 0.048 1546 Dihedral : 21.728 171.229 3112 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.79 % Allowed : 11.56 % Favored : 86.65 % 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 (0.28), residues: 954 helix: 1.77 (0.25), residues: 421 sheet: -1.02 (0.45), residues: 140 loop : -0.88 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 740 TYR 0.009 0.001 TYR A 857 PHE 0.014 0.001 PHE A 399 TRP 0.017 0.002 TRP A 486 HIS 0.006 0.001 HIS A 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (12124) covalent geometry : angle 0.88834 / 0.39 (17171) hydrogen bonds : bond 0.06765 / 8.03 ( 531) hydrogen bonds : angle 4.41963 / 5.46 ( 1371) *********************** 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 74 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 CYS cc_start: 0.8250 (m) cc_final: 0.7672 (t) REVERT: A 570 MET cc_start: 0.7882 (tpt) cc_final: 0.7613 (mmm) outliers start: 15 outliers final: 10 residues processed: 66 average time/residue: 0.0892 time to fit residues: 9.4480 Evaluate side-chains 66 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 934 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 0.3980 chunk 31 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 ASN A 375 GLN ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.092254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.066312 restraints weight = 44148.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.068348 restraints weight = 23804.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.069636 restraints weight = 16878.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.070373 restraints weight = 13872.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.070707 restraints weight = 12428.187| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12124 Z= 0.233 Angle : 0.933 11.631 17171 Z= 0.419 Chirality : 0.069 0.544 1979 Planarity : 0.005 0.048 1546 Dihedral : 21.941 170.260 3112 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.03 % Allowed : 13.11 % Favored : 84.86 % 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 (0.27), residues: 954 helix: 1.41 (0.25), residues: 417 sheet: -1.14 (0.44), residues: 143 loop : -1.11 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 736 TYR 0.015 0.002 TYR A 138 PHE 0.014 0.002 PHE A 399 TRP 0.014 0.002 TRP A 782 HIS 0.005 0.002 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.23 (12124) covalent geometry : angle 0.93327 / 0.42 (17171) hydrogen bonds : bond 0.07242 / 8.43 ( 531) hydrogen bonds : angle 4.52542 / 5.57 ( 1371) *********************** 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 76 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.377 Fit side-chains REVERT: A 134 CYS cc_start: 0.8244 (m) cc_final: 0.7688 (t) REVERT: A 486 TRP cc_start: 0.7104 (m-10) cc_final: 0.6676 (m-10) REVERT: A 570 MET cc_start: 0.7884 (tpt) cc_final: 0.7543 (mmm) REVERT: A 837 MET cc_start: 0.6149 (mmm) cc_final: 0.5700 (mmp) outliers start: 17 outliers final: 11 residues processed: 67 average time/residue: 0.0883 time to fit residues: 9.6424 Evaluate side-chains 65 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 934 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 31 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 561 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 = 0.3899 r_free = 0.3899 target = 0.092771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.066921 restraints weight = 43969.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.068943 restraints weight = 24233.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.070198 restraints weight = 17312.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.070877 restraints weight = 14317.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.071204 restraints weight = 12910.940| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12124 Z= 0.179 Angle : 0.871 11.085 17171 Z= 0.393 Chirality : 0.066 0.487 1979 Planarity : 0.005 0.050 1546 Dihedral : 21.910 171.857 3112 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.50 % Allowed : 13.59 % Favored : 83.91 % 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: 0.05 (0.27), residues: 954 helix: 1.49 (0.25), residues: 419 sheet: -1.09 (0.43), residues: 143 loop : -1.09 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 740 TYR 0.013 0.002 TYR A 138 PHE 0.014 0.001 PHE A 958 TRP 0.013 0.001 TRP A 782 HIS 0.006 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (12124) covalent geometry : angle 0.87115 / 0.39 (17171) hydrogen bonds : bond 0.06673 / 7.74 ( 531) hydrogen bonds : angle 4.41407 / 5.41 ( 1371) *********************** 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 82 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 134 CYS cc_start: 0.8195 (m) cc_final: 0.7633 (t) REVERT: A 486 TRP cc_start: 0.7067 (m-10) cc_final: 0.6618 (m-10) REVERT: A 570 MET cc_start: 0.7924 (tpt) cc_final: 0.7574 (mmm) REVERT: A 837 MET cc_start: 0.6279 (mmm) cc_final: 0.5865 (mmp) outliers start: 21 outliers final: 11 residues processed: 73 average time/residue: 0.0822 time to fit residues: 9.8550 Evaluate side-chains 70 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 934 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 33 optimal weight: 0.0030 chunk 62 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 561 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 = 0.3907 r_free = 0.3907 target = 0.093279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.067369 restraints weight = 43734.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.069467 restraints weight = 23519.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.070768 restraints weight = 16522.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.071547 restraints weight = 13551.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.071915 restraints weight = 12098.580| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12124 Z= 0.161 Angle : 0.840 10.194 17171 Z= 0.380 Chirality : 0.064 0.457 1979 Planarity : 0.004 0.051 1546 Dihedral : 21.876 172.496 3112 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.26 % Allowed : 13.95 % Favored : 83.79 % 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: 0.17 (0.28), residues: 954 helix: 1.58 (0.26), residues: 420 sheet: -1.00 (0.43), residues: 143 loop : -1.04 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 764 TYR 0.012 0.001 TYR A 138 PHE 0.033 0.002 PHE A 399 TRP 0.012 0.001 TRP A 782 HIS 0.008 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (12124) covalent geometry : angle 0.83999 / 0.38 (17171) hydrogen bonds : bond 0.06373 / 7.31 ( 531) hydrogen bonds : angle 4.33657 / 5.33 ( 1371) *********************** 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 81 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 134 CYS cc_start: 0.8247 (m) cc_final: 0.7672 (t) REVERT: A 486 TRP cc_start: 0.7066 (m-10) cc_final: 0.6709 (m-10) REVERT: A 489 ASP cc_start: 0.7760 (m-30) cc_final: 0.7476 (m-30) REVERT: A 570 MET cc_start: 0.7942 (tpt) cc_final: 0.7611 (mmm) REVERT: A 837 MET cc_start: 0.6231 (mmm) cc_final: 0.5805 (mmp) outliers start: 19 outliers final: 13 residues processed: 75 average time/residue: 0.0795 time to fit residues: 9.8538 Evaluate side-chains 73 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 840 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 0.4980 chunk 72 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 3 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 561 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 = 0.3929 r_free = 0.3929 target = 0.094438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.068481 restraints weight = 43883.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.070624 restraints weight = 23666.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.071928 restraints weight = 16583.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.072704 restraints weight = 13592.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.073106 restraints weight = 12143.059| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12124 Z= 0.138 Angle : 0.804 9.815 17171 Z= 0.363 Chirality : 0.062 0.421 1979 Planarity : 0.004 0.051 1546 Dihedral : 21.773 173.247 3112 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.55 % Allowed : 15.14 % Favored : 83.31 % 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 (0.28), residues: 954 helix: 1.75 (0.26), residues: 423 sheet: -0.91 (0.43), residues: 150 loop : -0.85 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 740 TYR 0.011 0.001 TYR A 418 PHE 0.013 0.001 PHE A 958 TRP 0.013 0.001 TRP A 598 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (12124) covalent geometry : angle 0.80411 / 0.36 (17171) hydrogen bonds : bond 0.06067 / 6.95 ( 531) hydrogen bonds : angle 4.19952 / 5.13 ( 1371) *********************** 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 74 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 134 CYS cc_start: 0.8171 (m) cc_final: 0.7675 (t) REVERT: A 489 ASP cc_start: 0.7808 (m-30) cc_final: 0.7463 (m-30) REVERT: A 570 MET cc_start: 0.8034 (tpt) cc_final: 0.7788 (mmm) REVERT: A 837 MET cc_start: 0.6092 (mmm) cc_final: 0.5623 (mmp) outliers start: 13 outliers final: 10 residues processed: 70 average time/residue: 0.0823 time to fit residues: 9.5558 Evaluate side-chains 69 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 857 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 64 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 4 optimal weight: 30.0000 chunk 55 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 561 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 = 0.3914 r_free = 0.3914 target = 0.093667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.067820 restraints weight = 43531.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.069903 restraints weight = 23571.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.071186 restraints weight = 16661.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.071965 restraints weight = 13700.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.072283 restraints weight = 12257.995| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12124 Z= 0.160 Angle : 0.817 9.901 17171 Z= 0.369 Chirality : 0.062 0.425 1979 Planarity : 0.004 0.051 1546 Dihedral : 21.781 172.093 3112 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.43 % Allowed : 15.26 % Favored : 83.31 % 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: 0.37 (0.28), residues: 954 helix: 1.71 (0.26), residues: 422 sheet: -1.04 (0.41), residues: 164 loop : -0.82 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 615 TYR 0.011 0.001 TYR A 698 PHE 0.017 0.001 PHE A 399 TRP 0.010 0.001 TRP A 782 HIS 0.006 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (12124) covalent geometry : angle 0.81749 / 0.37 (17171) hydrogen bonds : bond 0.06206 / 7.05 ( 531) hydrogen bonds : angle 4.20424 / 5.13 ( 1371) *********************** 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 71 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 134 CYS cc_start: 0.8181 (m) cc_final: 0.7687 (t) REVERT: A 489 ASP cc_start: 0.7739 (m-30) cc_final: 0.7442 (m-30) REVERT: A 570 MET cc_start: 0.7966 (tpt) cc_final: 0.7595 (mmm) REVERT: A 710 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7961 (mt-10) REVERT: A 837 MET cc_start: 0.6228 (mmm) cc_final: 0.5755 (mmp) outliers start: 12 outliers final: 12 residues processed: 66 average time/residue: 0.0795 time to fit residues: 8.6650 Evaluate side-chains 71 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 152 HIS Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 857 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 41 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 HIS ** A 561 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 = 0.3911 r_free = 0.3911 target = 0.093386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.067552 restraints weight = 43958.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.069616 restraints weight = 23681.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.070906 restraints weight = 16705.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.071640 restraints weight = 13719.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.072126 restraints weight = 12313.077| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12124 Z= 0.167 Angle : 0.832 9.637 17171 Z= 0.375 Chirality : 0.063 0.428 1979 Planarity : 0.004 0.049 1546 Dihedral : 21.798 171.776 3112 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.31 % Allowed : 15.73 % Favored : 82.96 % 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: 0.25 (0.28), residues: 954 helix: 1.64 (0.26), residues: 421 sheet: -1.06 (0.41), residues: 160 loop : -0.93 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 642 TYR 0.011 0.001 TYR A 138 PHE 0.018 0.001 PHE A 156 TRP 0.011 0.001 TRP A 782 HIS 0.006 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (12124) covalent geometry : angle 0.83213 / 0.37 (17171) hydrogen bonds : bond 0.06297 / 7.16 ( 531) hydrogen bonds : angle 4.25298 / 5.19 ( 1371) ********************** 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 70 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 CYS cc_start: 0.8122 (m) cc_final: 0.7609 (t) REVERT: A 570 MET cc_start: 0.8028 (tpt) cc_final: 0.7622 (mmm) REVERT: A 710 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7949 (mt-10) REVERT: A 837 MET cc_start: 0.6358 (mmm) cc_final: 0.5887 (mmp) outliers start: 11 outliers final: 10 residues processed: 66 average time/residue: 0.0837 time to fit residues: 9.2292 Evaluate side-chains 68 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 857 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 45 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.094698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.068819 restraints weight = 43800.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.070955 restraints weight = 23615.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.072286 restraints weight = 16599.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.072932 restraints weight = 13562.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.073510 restraints weight = 12236.525| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12124 Z= 0.134 Angle : 0.788 9.465 17171 Z= 0.356 Chirality : 0.061 0.413 1979 Planarity : 0.004 0.053 1546 Dihedral : 21.671 173.296 3112 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.07 % Allowed : 16.09 % Favored : 82.84 % 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: 0.51 (0.29), residues: 954 helix: 1.83 (0.26), residues: 422 sheet: -0.89 (0.42), residues: 160 loop : -0.78 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 740 TYR 0.008 0.001 TYR A 74 PHE 0.016 0.001 PHE A 399 TRP 0.013 0.001 TRP A 598 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (12124) covalent geometry : angle 0.78819 / 0.36 (17171) hydrogen bonds : bond 0.05935 / 6.76 ( 531) hydrogen bonds : angle 4.11982 / 5.04 ( 1371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2460.38 seconds wall clock time: 43 minutes 15.89 seconds (2595.89 seconds total)