Starting phenix.real_space_refine on Thu Mar 5 22:43:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x3v_32994/03_2026/7x3v_32994.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x3v_32994/03_2026/7x3v_32994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x3v_32994/03_2026/7x3v_32994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x3v_32994/03_2026/7x3v_32994.map" model { file = "/net/cci-nas-00/data/ceres_data/7x3v_32994/03_2026/7x3v_32994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x3v_32994/03_2026/7x3v_32994.cif" } resolution = 3.09 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 Anisotropic ADP refinement not supported. Converting 11879 atoms to isotropic. 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 292 5.49 5 S 27 5.16 5 C 9716 2.51 5 N 3053 2.21 5 O 3711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16799 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2978 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3008 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "U" Number of atoms: 4840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4840 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 38, 'TRANS': 551} Chain breaks: 1 Time building chain proxies: 3.42, per 1000 atoms: 0.20 Number of scatterers: 16799 At special positions: 0 Unit cell: (139.642, 124.487, 146.137, 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 27 16.00 P 292 15.00 O 3711 8.00 N 3053 7.00 C 9716 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: 1.43 Conformation dependent library (CDL) restraints added in 537.0 milliseconds 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2564 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 11 sheets defined 64.6% alpha, 2.7% beta 144 base pairs and 265 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.511A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.636A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.535A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.541A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.546A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.526A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.548A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.757A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.540A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.515A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.521A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 178 through 192 Processing helix chain 'U' and resid 193 through 196 Processing helix chain 'U' and resid 197 through 202 removed outlier: 3.566A pdb=" N GLN U 201 " --> pdb=" O HIS U 197 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN U 202 " --> pdb=" O SER U 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 197 through 202' Processing helix chain 'U' and resid 204 through 213 Processing helix chain 'U' and resid 237 through 241 Processing helix chain 'U' and resid 243 through 267 removed outlier: 3.588A pdb=" N ILE U 247 " --> pdb=" O ALA U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 283 through 288 Processing helix chain 'U' and resid 295 through 310 removed outlier: 4.472A pdb=" N ARG U 307 " --> pdb=" O ARG U 303 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU U 308 " --> pdb=" O LEU U 304 " (cutoff:3.500A) Processing helix chain 'U' and resid 312 through 316 removed outlier: 3.564A pdb=" N ARG U 316 " --> pdb=" O ARG U 313 " (cutoff:3.500A) Processing helix chain 'U' and resid 368 through 376 removed outlier: 6.065A pdb=" N ARG U 373 " --> pdb=" O LEU U 370 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU U 374 " --> pdb=" O TYR U 371 " (cutoff:3.500A) Processing helix chain 'U' and resid 384 through 403 Processing helix chain 'U' and resid 403 through 415 removed outlier: 3.697A pdb=" N TYR U 411 " --> pdb=" O HIS U 407 " (cutoff:3.500A) Processing helix chain 'U' and resid 430 through 435 Processing helix chain 'U' and resid 436 through 460 Processing helix chain 'U' and resid 461 through 469 removed outlier: 3.598A pdb=" N LYS U 469 " --> pdb=" O VAL U 465 " (cutoff:3.500A) Processing helix chain 'U' and resid 474 through 492 removed outlier: 4.598A pdb=" N LEU U 480 " --> pdb=" O LEU U 476 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 510 removed outlier: 4.341A pdb=" N ASP U 499 " --> pdb=" O LYS U 495 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU U 500 " --> pdb=" O SER U 496 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU U 502 " --> pdb=" O LYS U 498 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE U 503 " --> pdb=" O ASP U 499 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASP U 507 " --> pdb=" O PHE U 503 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS U 508 " --> pdb=" O SER U 504 " (cutoff:3.500A) Processing helix chain 'U' and resid 524 through 528 removed outlier: 3.679A pdb=" N SER U 527 " --> pdb=" O ASN U 524 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU U 528 " --> pdb=" O PRO U 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 524 through 528' Processing helix chain 'U' and resid 568 through 581 Processing helix chain 'U' and resid 585 through 592 Processing helix chain 'U' and resid 607 through 618 Processing helix chain 'U' and resid 633 through 649 removed outlier: 3.823A pdb=" N TYR U 646 " --> pdb=" O GLU U 642 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS U 647 " --> pdb=" O PHE U 643 " (cutoff:3.500A) Processing helix chain 'U' and resid 651 through 656 Processing helix chain 'U' and resid 681 through 686 removed outlier: 3.616A pdb=" N ILE U 685 " --> pdb=" O ASN U 681 " (cutoff:3.500A) Processing helix chain 'U' and resid 695 through 727 removed outlier: 4.548A pdb=" N ALA U 699 " --> pdb=" O LYS U 695 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE U 715 " --> pdb=" O SER U 711 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE U 716 " --> pdb=" O ASP U 712 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL U 725 " --> pdb=" O GLU U 721 " (cutoff:3.500A) Processing helix chain 'U' and resid 732 through 743 removed outlier: 3.896A pdb=" N GLN U 736 " --> pdb=" O PRO U 732 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE U 740 " --> pdb=" O GLN U 736 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.076A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.302A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.745A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.016A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.142A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'U' and resid 174 through 175 removed outlier: 6.824A pdb=" N LEU U 603 " --> pdb=" O LEU U 630 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY U 547 " --> pdb=" O ARG U 542 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ARG U 542 " --> pdb=" O GLY U 547 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE U 549 " --> pdb=" O LEU U 540 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 265 stacking parallelities Total time for adding SS restraints: 3.88 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2752 1.32 - 1.44: 5689 1.44 - 1.56: 8657 1.56 - 1.68: 582 1.68 - 1.80: 48 Bond restraints: 17728 Sorted by residual: bond pdb=" N ARG H 30 " pdb=" CA ARG H 30 " ideal model delta sigma weight residual 1.454 1.484 -0.029 1.17e-02 7.31e+03 6.35e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.52e+00 bond pdb=" CG1 ILE H 58 " pdb=" CD1 ILE H 58 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.22e+00 bond pdb=" CB GLN A 76 " pdb=" CG GLN A 76 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.93e+00 bond pdb=" CB ARG B 35 " pdb=" CG ARG B 35 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.61e+00 ... (remaining 17723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 23977 1.66 - 3.32: 1126 3.32 - 4.98: 96 4.98 - 6.63: 17 6.63 - 8.29: 4 Bond angle restraints: 25220 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.71 109.00 4.71 9.50e-01 1.11e+00 2.46e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 120.20 124.55 -4.35 1.50e+00 4.44e-01 8.39e+00 angle pdb=" N THR U 155 " pdb=" CA THR U 155 " pdb=" CB THR U 155 " ideal model delta sigma weight residual 113.65 109.54 4.11 1.47e+00 4.63e-01 7.83e+00 angle pdb=" N THR U 155 " pdb=" CA THR U 155 " pdb=" C THR U 155 " ideal model delta sigma weight residual 113.72 109.53 4.19 1.52e+00 4.33e-01 7.59e+00 angle pdb=" NE ARG D 76 " pdb=" CZ ARG D 76 " pdb=" NH1 ARG D 76 " ideal model delta sigma weight residual 121.50 118.84 2.66 1.00e+00 1.00e+00 7.09e+00 ... (remaining 25215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 8412 34.99 - 69.99: 1507 69.99 - 104.98: 26 104.98 - 139.98: 1 139.98 - 174.97: 3 Dihedral angle restraints: 9949 sinusoidal: 5990 harmonic: 3959 Sorted by residual: dihedral pdb=" CA ASN U 269 " pdb=" C ASN U 269 " pdb=" N PHE U 270 " pdb=" CA PHE U 270 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLU U 268 " pdb=" C GLU U 268 " pdb=" N ASN U 269 " pdb=" CA ASN U 269 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA TYR U 355 " pdb=" C TYR U 355 " pdb=" N THR U 356 " pdb=" CA THR U 356 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 9946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1421 0.033 - 0.067: 937 0.067 - 0.100: 381 0.100 - 0.133: 82 0.133 - 0.166: 15 Chirality restraints: 2836 Sorted by residual: chirality pdb=" CA PRO B 32 " pdb=" N PRO B 32 " pdb=" C PRO B 32 " pdb=" CB PRO B 32 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CG LEU U 235 " pdb=" CB LEU U 235 " pdb=" CD1 LEU U 235 " pdb=" CD2 LEU U 235 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" C4' DG J 68 " pdb=" C5' DG J 68 " pdb=" O4' DG J 68 " pdb=" C3' DG J 68 " both_signs ideal model delta sigma weight residual False -2.53 -2.37 -0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 2833 not shown) Planarity restraints: 2201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE U 151 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO U 152 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO U 152 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO U 152 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 99 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO H 100 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 99 " 0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO D 100 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " 0.035 5.00e-02 4.00e+02 ... (remaining 2198 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 671 2.69 - 3.24: 15572 3.24 - 3.79: 29866 3.79 - 4.35: 39670 4.35 - 4.90: 57576 Nonbonded interactions: 143355 Sorted by model distance: nonbonded pdb=" OG1 THR U 426 " pdb=" OE1 GLN U 427 " model vdw 2.135 3.040 nonbonded pdb=" NZ LYS U 418 " pdb=" O ASP U 419 " model vdw 2.140 3.120 nonbonded pdb=" NZ LYS U 445 " pdb=" O LYS U 498 " model vdw 2.209 3.120 nonbonded pdb=" O SER U 401 " pdb=" ND1 HIS U 407 " model vdw 2.243 3.120 nonbonded pdb=" O PRO U 430 " pdb=" OG1 THR U 433 " model vdw 2.246 3.040 ... (remaining 143350 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.770 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.011 0.081 17728 Z= 0.465 Angle : 0.771 8.293 25220 Z= 0.448 Chirality : 0.048 0.166 2836 Planarity : 0.006 0.072 2201 Dihedral : 25.591 174.973 7385 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -0.80 (0.22), residues: 1331 helix: 0.49 (0.18), residues: 808 sheet: -0.60 (1.25), residues: 10 loop : -2.21 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 76 TYR 0.038 0.003 TYR G 50 PHE 0.033 0.003 PHE U 208 TRP 0.022 0.002 TRP U 509 HIS 0.008 0.002 HIS U 555 Details of bonding type rmsd covalent geometry : bond 0.01073 (17728) covalent geometry : angle 0.77083 (25220) hydrogen bonds : bond 0.12236 ( 979) hydrogen bonds : angle 4.87029 ( 2507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.506 Fit side-chains REVERT: G 64 GLU cc_start: 0.8599 (tt0) cc_final: 0.8370 (tt0) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1406 time to fit residues: 23.1108 Evaluate side-chains 109 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.1980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 407 HIS ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 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 = 0.3858 r_free = 0.3858 target = 0.110454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.067868 restraints weight = 41003.054| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.72 r_work: 0.2835 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17728 Z= 0.159 Angle : 0.592 7.080 25220 Z= 0.343 Chirality : 0.036 0.128 2836 Planarity : 0.005 0.064 2201 Dihedral : 28.980 173.007 4673 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % 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: 0.29 (0.23), residues: 1331 helix: 1.42 (0.18), residues: 813 sheet: None (None), residues: 0 loop : -1.88 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 96 TYR 0.017 0.001 TYR H 37 PHE 0.015 0.001 PHE U 539 TRP 0.007 0.001 TRP U 509 HIS 0.003 0.001 HIS U 407 Details of bonding type rmsd covalent geometry : bond 0.00344 (17728) covalent geometry : angle 0.59166 (25220) hydrogen bonds : bond 0.04829 ( 979) hydrogen bonds : angle 3.65214 ( 2507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8633 (m110) cc_final: 0.8276 (t0) REVERT: G 64 GLU cc_start: 0.9225 (tt0) cc_final: 0.9007 (tt0) outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 0.1317 time to fit residues: 24.1241 Evaluate side-chains 113 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 113 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN F 25 ASN ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 606 HIS ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 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 = 0.3848 r_free = 0.3848 target = 0.110038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.067026 restraints weight = 41337.733| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.43 r_work: 0.2812 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17728 Z= 0.204 Angle : 0.582 7.209 25220 Z= 0.336 Chirality : 0.037 0.127 2836 Planarity : 0.005 0.061 2201 Dihedral : 28.757 173.481 4673 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.52 % Allowed : 6.47 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.23), residues: 1331 helix: 1.74 (0.19), residues: 811 sheet: None (None), residues: 0 loop : -1.72 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 77 TYR 0.017 0.001 TYR H 37 PHE 0.013 0.002 PHE U 208 TRP 0.004 0.001 TRP U 509 HIS 0.004 0.001 HIS U 407 Details of bonding type rmsd covalent geometry : bond 0.00463 (17728) covalent geometry : angle 0.58186 (25220) hydrogen bonds : bond 0.04544 ( 979) hydrogen bonds : angle 3.42791 ( 2507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.529 Fit side-chains REVERT: C 73 ASN cc_start: 0.8584 (m110) cc_final: 0.8320 (t0) REVERT: D 37 TYR cc_start: 0.9548 (m-80) cc_final: 0.9305 (m-80) REVERT: G 64 GLU cc_start: 0.9288 (tt0) cc_final: 0.9077 (tt0) outliers start: 6 outliers final: 5 residues processed: 121 average time/residue: 0.1318 time to fit residues: 24.3302 Evaluate side-chains 121 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain U residue 571 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 93 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 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 = 0.3856 r_free = 0.3856 target = 0.110396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.067287 restraints weight = 41247.115| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.75 r_work: 0.2822 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17728 Z= 0.178 Angle : 0.558 7.086 25220 Z= 0.324 Chirality : 0.035 0.129 2836 Planarity : 0.005 0.054 2201 Dihedral : 28.622 174.769 4673 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.86 % Allowed : 6.90 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1331 helix: 1.92 (0.19), residues: 810 sheet: None (None), residues: 0 loop : -1.61 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 77 TYR 0.014 0.001 TYR U 238 PHE 0.012 0.001 PHE U 539 TRP 0.003 0.001 TRP U 627 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00400 (17728) covalent geometry : angle 0.55789 (25220) hydrogen bonds : bond 0.04255 ( 979) hydrogen bonds : angle 3.31204 ( 2507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.390 Fit side-chains REVERT: C 73 ASN cc_start: 0.8554 (m110) cc_final: 0.8349 (t0) REVERT: U 606 HIS cc_start: 0.6250 (OUTLIER) cc_final: 0.5926 (t70) outliers start: 10 outliers final: 7 residues processed: 122 average time/residue: 0.1257 time to fit residues: 23.7524 Evaluate side-chains 119 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain U residue 396 THR Chi-restraints excluded: chain U residue 571 ASN Chi-restraints excluded: chain U residue 606 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 105 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 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 = 0.3860 r_free = 0.3860 target = 0.110321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.069737 restraints weight = 41109.284| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.15 r_work: 0.2817 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17728 Z= 0.180 Angle : 0.556 7.076 25220 Z= 0.322 Chirality : 0.036 0.152 2836 Planarity : 0.005 0.054 2201 Dihedral : 28.555 177.661 4673 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.95 % Allowed : 8.19 % Favored : 90.86 % 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: 1.06 (0.24), residues: 1331 helix: 2.01 (0.19), residues: 810 sheet: None (None), residues: 0 loop : -1.50 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 77 TYR 0.016 0.001 TYR D 80 PHE 0.013 0.001 PHE U 590 TRP 0.005 0.001 TRP U 627 HIS 0.003 0.001 HIS U 407 Details of bonding type rmsd covalent geometry : bond 0.00406 (17728) covalent geometry : angle 0.55554 (25220) hydrogen bonds : bond 0.04188 ( 979) hydrogen bonds : angle 3.24241 ( 2507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.532 Fit side-chains REVERT: U 606 HIS cc_start: 0.6066 (OUTLIER) cc_final: 0.5783 (t70) outliers start: 11 outliers final: 8 residues processed: 119 average time/residue: 0.1288 time to fit residues: 23.5514 Evaluate side-chains 121 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain U residue 396 THR Chi-restraints excluded: chain U residue 571 ASN Chi-restraints excluded: chain U residue 590 PHE Chi-restraints excluded: chain U residue 606 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 131 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 149 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 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 = 0.3864 r_free = 0.3864 target = 0.110568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.070895 restraints weight = 40942.598| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.22 r_work: 0.2822 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17728 Z= 0.155 Angle : 0.548 6.983 25220 Z= 0.318 Chirality : 0.035 0.131 2836 Planarity : 0.004 0.052 2201 Dihedral : 28.544 177.780 4673 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.21 % Allowed : 8.28 % Favored : 90.52 % 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: 1.12 (0.24), residues: 1331 helix: 2.03 (0.19), residues: 815 sheet: None (None), residues: 0 loop : -1.45 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 77 TYR 0.013 0.001 TYR U 238 PHE 0.012 0.001 PHE U 590 TRP 0.005 0.001 TRP U 627 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00342 (17728) covalent geometry : angle 0.54790 (25220) hydrogen bonds : bond 0.04074 ( 979) hydrogen bonds : angle 3.22260 ( 2507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.509 Fit side-chains REVERT: U 606 HIS cc_start: 0.6026 (OUTLIER) cc_final: 0.5712 (t70) outliers start: 14 outliers final: 10 residues processed: 122 average time/residue: 0.1309 time to fit residues: 24.2777 Evaluate side-chains 123 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain U residue 396 THR Chi-restraints excluded: chain U residue 543 VAL Chi-restraints excluded: chain U residue 571 ASN Chi-restraints excluded: chain U residue 590 PHE Chi-restraints excluded: chain U residue 606 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 43 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 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 = 0.3863 r_free = 0.3863 target = 0.110478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.069905 restraints weight = 40930.293| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.18 r_work: 0.2821 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17728 Z= 0.176 Angle : 0.549 7.039 25220 Z= 0.319 Chirality : 0.035 0.145 2836 Planarity : 0.004 0.052 2201 Dihedral : 28.495 179.920 4673 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.03 % Allowed : 9.05 % Favored : 89.91 % 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: 1.19 (0.24), residues: 1331 helix: 2.09 (0.19), residues: 810 sheet: None (None), residues: 0 loop : -1.40 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.018 0.001 TYR D 80 PHE 0.012 0.001 PHE U 590 TRP 0.004 0.001 TRP U 627 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00396 (17728) covalent geometry : angle 0.54872 (25220) hydrogen bonds : bond 0.04099 ( 979) hydrogen bonds : angle 3.18967 ( 2507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.404 Fit side-chains REVERT: U 606 HIS cc_start: 0.6078 (OUTLIER) cc_final: 0.5753 (t70) outliers start: 12 outliers final: 11 residues processed: 123 average time/residue: 0.1296 time to fit residues: 24.4812 Evaluate side-chains 128 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain U residue 396 THR Chi-restraints excluded: chain U residue 543 VAL Chi-restraints excluded: chain U residue 555 HIS Chi-restraints excluded: chain U residue 571 ASN Chi-restraints excluded: chain U residue 590 PHE Chi-restraints excluded: chain U residue 606 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 156 optimal weight: 0.9980 chunk 118 optimal weight: 0.4980 chunk 119 optimal weight: 0.0980 chunk 108 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 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 = 0.3868 r_free = 0.3868 target = 0.110783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.067981 restraints weight = 41231.502| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.75 r_work: 0.2847 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17728 Z= 0.148 Angle : 0.546 6.963 25220 Z= 0.317 Chirality : 0.034 0.133 2836 Planarity : 0.004 0.053 2201 Dihedral : 28.494 179.998 4673 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.12 % Allowed : 9.14 % Favored : 89.74 % 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: 1.24 (0.24), residues: 1331 helix: 2.10 (0.19), residues: 815 sheet: None (None), residues: 0 loop : -1.36 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.024 0.001 TYR U 300 PHE 0.011 0.001 PHE U 590 TRP 0.004 0.001 TRP U 627 HIS 0.002 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00325 (17728) covalent geometry : angle 0.54557 (25220) hydrogen bonds : bond 0.03994 ( 979) hydrogen bonds : angle 3.17150 ( 2507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.429 Fit side-chains REVERT: U 606 HIS cc_start: 0.6311 (OUTLIER) cc_final: 0.5957 (t70) outliers start: 13 outliers final: 10 residues processed: 125 average time/residue: 0.1269 time to fit residues: 24.3353 Evaluate side-chains 127 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain U residue 396 THR Chi-restraints excluded: chain U residue 543 VAL Chi-restraints excluded: chain U residue 555 HIS Chi-restraints excluded: chain U residue 571 ASN Chi-restraints excluded: chain U residue 590 PHE Chi-restraints excluded: chain U residue 606 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 31 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.111118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.068421 restraints weight = 40948.361| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.69 r_work: 0.2856 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17728 Z= 0.148 Angle : 0.546 11.099 25220 Z= 0.316 Chirality : 0.034 0.133 2836 Planarity : 0.004 0.053 2201 Dihedral : 28.452 179.758 4673 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.03 % Allowed : 9.22 % Favored : 89.74 % 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: 1.28 (0.24), residues: 1331 helix: 2.12 (0.19), residues: 815 sheet: None (None), residues: 0 loop : -1.33 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 77 TYR 0.016 0.001 TYR U 300 PHE 0.011 0.001 PHE U 539 TRP 0.004 0.001 TRP U 627 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00323 (17728) covalent geometry : angle 0.54632 (25220) hydrogen bonds : bond 0.03934 ( 979) hydrogen bonds : angle 3.14945 ( 2507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.512 Fit side-chains REVERT: U 606 HIS cc_start: 0.6253 (OUTLIER) cc_final: 0.5903 (t70) outliers start: 12 outliers final: 10 residues processed: 123 average time/residue: 0.1297 time to fit residues: 24.3534 Evaluate side-chains 126 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain U residue 396 THR Chi-restraints excluded: chain U residue 543 VAL Chi-restraints excluded: chain U residue 555 HIS Chi-restraints excluded: chain U residue 571 ASN Chi-restraints excluded: chain U residue 590 PHE Chi-restraints excluded: chain U residue 606 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 133 optimal weight: 0.3980 chunk 149 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 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 = 0.3853 r_free = 0.3853 target = 0.110212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.067176 restraints weight = 40701.226| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.66 r_work: 0.2821 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17728 Z= 0.188 Angle : 0.554 7.008 25220 Z= 0.321 Chirality : 0.036 0.133 2836 Planarity : 0.004 0.052 2201 Dihedral : 28.499 177.703 4673 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.03 % Allowed : 9.48 % Favored : 89.48 % 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: 1.24 (0.24), residues: 1331 helix: 2.07 (0.19), residues: 816 sheet: None (None), residues: 0 loop : -1.32 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 77 TYR 0.012 0.001 TYR D 80 PHE 0.011 0.001 PHE U 590 TRP 0.004 0.001 TRP U 627 HIS 0.003 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00426 (17728) covalent geometry : angle 0.55436 (25220) hydrogen bonds : bond 0.04193 ( 979) hydrogen bonds : angle 3.18965 ( 2507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.447 Fit side-chains REVERT: U 606 HIS cc_start: 0.6293 (OUTLIER) cc_final: 0.5930 (t70) outliers start: 12 outliers final: 10 residues processed: 124 average time/residue: 0.1244 time to fit residues: 23.6460 Evaluate side-chains 127 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain U residue 396 THR Chi-restraints excluded: chain U residue 543 VAL Chi-restraints excluded: chain U residue 555 HIS Chi-restraints excluded: chain U residue 571 ASN Chi-restraints excluded: chain U residue 590 PHE Chi-restraints excluded: chain U residue 606 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 108 optimal weight: 0.9980 chunk 150 optimal weight: 0.4980 chunk 140 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 0.0030 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 688 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 = 0.3867 r_free = 0.3867 target = 0.110734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.067868 restraints weight = 40819.697| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.75 r_work: 0.2845 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17728 Z= 0.148 Angle : 0.550 6.942 25220 Z= 0.319 Chirality : 0.035 0.135 2836 Planarity : 0.004 0.052 2201 Dihedral : 28.505 177.682 4673 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.21 % Allowed : 9.48 % Favored : 89.31 % 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: 1.29 (0.24), residues: 1331 helix: 2.11 (0.19), residues: 816 sheet: None (None), residues: 0 loop : -1.28 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.028 0.001 TYR U 300 PHE 0.011 0.001 PHE U 590 TRP 0.003 0.001 TRP U 627 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00325 (17728) covalent geometry : angle 0.55034 (25220) hydrogen bonds : bond 0.04065 ( 979) hydrogen bonds : angle 3.17303 ( 2507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5373.66 seconds wall clock time: 91 minutes 53.66 seconds (5513.66 seconds total)