Starting phenix.real_space_refine on Sat Sep 12 13:09:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7enn_31217/09_2026/7enn_31217.cif Found real_map, /net/cci-nas-00/data/ceres_data/7enn_31217/09_2026/7enn_31217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7enn_31217/09_2026/7enn_31217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7enn_31217/09_2026/7enn_31217.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7enn_31217/09_2026/7enn_31217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7enn_31217/09_2026/7enn_31217.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7enn_31217/09_2026/7enn_31217.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7enn_31217/09_2026/7enn_31217.cif" } resolution = 2.8 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= 0.001 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: 7 Type Number sf(0) Gaussians P 294 5.49 5 S 31 5.16 5 Be 1 3.05 5 C 9365 2.51 5 N 2989 2.21 5 O 3636 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 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: 16319 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 4315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4315 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 14, 'TRANS': 524} Chain breaks: 4 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 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: "L" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} 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: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 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: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 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: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} 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: "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: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 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: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.13, per 1000 atoms: 0.19 Number of scatterers: 16319 At special positions: 0 Unit cell: (143.431, 126.652, 115.286, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 31 16.00 P 294 15.00 F 3 9.00 O 3636 8.00 N 2989 7.00 C 9365 6.00 Be 1 4.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 488.1 milliseconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 63.5% alpha, 5.4% beta 145 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'K' and resid 32 through 40 removed outlier: 3.711A pdb=" N LEU K 36 " --> pdb=" O GLN K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 64 Processing helix chain 'K' and resid 76 through 91 Processing helix chain 'K' and resid 103 through 105 No H-bonds generated for 'chain 'K' and resid 103 through 105' Processing helix chain 'K' and resid 106 through 118 removed outlier: 3.576A pdb=" N GLN K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 138 Processing helix chain 'K' and resid 153 through 159 Processing helix chain 'K' and resid 161 through 165 Processing helix chain 'K' and resid 175 through 179 Processing helix chain 'K' and resid 184 through 192 removed outlier: 3.750A pdb=" N GLU K 192 " --> pdb=" O LYS K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 221 Processing helix chain 'K' and resid 226 through 228 No H-bonds generated for 'chain 'K' and resid 226 through 228' Processing helix chain 'K' and resid 229 through 237 removed outlier: 3.560A pdb=" N TYR K 237 " --> pdb=" O PHE K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 254 removed outlier: 3.867A pdb=" N GLU K 249 " --> pdb=" O GLU K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 296 Processing helix chain 'K' and resid 313 through 324 removed outlier: 3.947A pdb=" N GLN K 317 " --> pdb=" O ASN K 313 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 332 removed outlier: 4.781A pdb=" N ASP K 329 " --> pdb=" O TYR K 326 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY K 330 " --> pdb=" O LEU K 327 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL K 331 " --> pdb=" O PHE K 328 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU K 332 " --> pdb=" O ASP K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 363 Processing helix chain 'K' and resid 372 through 387 removed outlier: 3.511A pdb=" N LEU K 376 " --> pdb=" O MET K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 399 through 412 removed outlier: 3.943A pdb=" N HIS K 403 " --> pdb=" O GLY K 399 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY K 410 " --> pdb=" O ILE K 406 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN K 412 " --> pdb=" O ASN K 408 " (cutoff:3.500A) Processing helix chain 'K' and resid 421 through 425 Processing helix chain 'K' and resid 444 through 454 removed outlier: 4.237A pdb=" N ASP K 448 " --> pdb=" O ASN K 444 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 488 removed outlier: 3.562A pdb=" N ILE K 478 " --> pdb=" O THR K 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 489 through 498 removed outlier: 3.931A pdb=" N ILE K 493 " --> pdb=" O LEU K 489 " (cutoff:3.500A) Processing helix chain 'K' and resid 536 through 545 removed outlier: 3.964A pdb=" N SER K 540 " --> pdb=" O ILE K 536 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU K 542 " --> pdb=" O LEU K 538 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY K 543 " --> pdb=" O GLU K 539 " (cutoff:3.500A) Processing helix chain 'K' and resid 586 through 599 Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.590A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'L' and resid 24 through 29 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 3.762A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA L 76 " --> pdb=" O TYR L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 removed outlier: 3.507A pdb=" N VAL L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.618A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.552A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 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 removed outlier: 3.749A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.559A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 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: 3.721A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.556A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 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 Processing sheet with id=AA1, first strand: chain 'K' and resid 123 through 125 removed outlier: 6.289A pdb=" N VAL K 124 " --> pdb=" O LEU K 150 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR K 152 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE K 98 " --> pdb=" O LEU K 149 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N THR K 151 " --> pdb=" O PHE K 98 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE K 100 " --> pdb=" O THR K 151 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU K 99 " --> pdb=" O VAL K 172 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU K 171 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU K 201 " --> pdb=" O LEU K 171 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL K 173 " --> pdb=" O LEU K 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 390 through 393 removed outlier: 6.163A pdb=" N GLU K 391 " --> pdb=" O LEU K 418 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N SER K 420 " --> pdb=" O GLU K 391 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL K 393 " --> pdb=" O SER K 420 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL K 366 " --> pdb=" O PHE K 417 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU K 419 " --> pdb=" O VAL K 366 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU K 368 " --> pdb=" O LEU K 419 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL K 436 " --> pdb=" O ILE K 467 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LEU K 469 " --> pdb=" O VAL K 436 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE K 438 " --> pdb=" O LEU K 469 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY K 471 " --> pdb=" O PHE K 438 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS K 280 " --> pdb=" O ILE K 470 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.754A pdb=" N ARG A 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'L' and resid 96 through 98 removed outlier: 6.556A pdb=" N THR L 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.105A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.727A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.719A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.311A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 574 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 1.83 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: 3473 1.33 - 1.45: 4922 1.45 - 1.57: 8170 1.57 - 1.69: 586 1.69 - 1.81: 54 Bond restraints: 17205 Sorted by residual: bond pdb=" F2 BEF K 902 " pdb="BE BEF K 902 " ideal model delta sigma weight residual 1.476 1.705 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" F1 BEF K 902 " pdb="BE BEF K 902 " ideal model delta sigma weight residual 1.476 1.700 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" F3 BEF K 902 " pdb="BE BEF K 902 " ideal model delta sigma weight residual 1.476 1.690 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C3' DT J 7 " pdb=" C2' DT J 7 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.77e+00 ... (remaining 17200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 24440 4.21 - 8.42: 39 8.42 - 12.64: 3 12.64 - 16.85: 1 16.85 - 21.06: 1 Bond angle restraints: 24484 Sorted by residual: angle pdb=" F1 BEF K 902 " pdb="BE BEF K 902 " pdb=" F3 BEF K 902 " ideal model delta sigma weight residual 120.12 99.06 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" F2 BEF K 902 " pdb="BE BEF K 902 " pdb=" F3 BEF K 902 " ideal model delta sigma weight residual 119.96 105.13 14.83 3.00e+00 1.11e-01 2.44e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 24479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 8134 35.15 - 70.31: 1435 70.31 - 105.46: 9 105.46 - 140.61: 3 140.61 - 175.77: 3 Dihedral angle restraints: 9584 sinusoidal: 5825 harmonic: 3759 Sorted by residual: dihedral pdb=" C5' ADP K 901 " pdb=" O5' ADP K 901 " pdb=" PA ADP K 901 " pdb=" O2A ADP K 901 " ideal model delta sinusoidal sigma weight residual -60.00 115.77 -175.77 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP K 901 " pdb=" O3A ADP K 901 " pdb=" PA ADP K 901 " pdb=" PB ADP K 901 " ideal model delta sinusoidal sigma weight residual -60.00 65.01 -125.01 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" O1B ADP K 901 " pdb=" O3A ADP K 901 " pdb=" PB ADP K 901 " pdb=" PA ADP K 901 " ideal model delta sinusoidal sigma weight residual -60.00 58.31 -118.31 1 2.00e+01 2.50e-03 3.54e+01 ... (remaining 9581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1737 0.037 - 0.074: 741 0.074 - 0.111: 249 0.111 - 0.147: 40 0.147 - 0.184: 5 Chirality restraints: 2772 Sorted by residual: chirality pdb=" C3' DC J 126 " pdb=" C4' DC J 126 " pdb=" O3' DC J 126 " pdb=" C2' DC J 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" C3' DA I 98 " pdb=" C4' DA I 98 " pdb=" O3' DA I 98 " pdb=" C2' DA I 98 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CB ILE H 91 " pdb=" CA ILE H 91 " pdb=" CG1 ILE H 91 " pdb=" CG2 ILE H 91 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 2769 not shown) Planarity restraints: 2097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN K 444 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO K 445 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 445 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 445 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 168 " 0.012 2.00e-02 2.50e+03 1.18e-02 3.46e+00 pdb=" CG TRP K 168 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP K 168 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP K 168 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP K 168 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP K 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 168 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 168 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 168 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP K 168 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 517 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C ILE K 517 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE K 517 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU K 518 " 0.011 2.00e-02 2.50e+03 ... (remaining 2094 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 452 2.68 - 3.24: 14197 3.24 - 3.79: 28708 3.79 - 4.35: 38713 4.35 - 4.90: 56736 Nonbonded interactions: 138806 Sorted by model distance: nonbonded pdb=" N2 DG I 13 " pdb=" O2 DC J 135 " model vdw 2.127 2.496 nonbonded pdb=" OH TYR K 153 " pdb=" O ASP K 174 " model vdw 2.170 3.040 nonbonded pdb=" OH TYR K 214 " pdb=" O SER K 226 " model vdw 2.179 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.190 3.040 nonbonded pdb=" O SER K 244 " pdb=" OG SER K 248 " model vdw 2.205 3.040 ... (remaining 138801 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 '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)) } ncs_group { reference = (chain 'F' and resid 23 through 101) selection = (chain 'L' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) } 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: 10.130 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: 0.680 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.150 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:9.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.821 17208 Z= 0.927 Angle : 0.800 21.061 24484 Z= 0.647 Chirality : 0.045 0.184 2772 Planarity : 0.004 0.049 2097 Dihedral : 25.221 175.768 7160 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.23), residues: 1274 helix: 1.02 (0.18), residues: 789 sheet: -0.83 (0.64), residues: 80 loop : -2.24 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 145 TYR 0.023 0.002 TYR G 50 PHE 0.015 0.002 PHE K 409 TRP 0.031 0.003 TRP K 168 HIS 0.003 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.54 (17205) covalent geometry : angle 0.79978 / 0.65 (24484) hydrogen bonds : bond 0.12383 / 7.78 ( 945) hydrogen bonds : angle 4.27816 / 3.00 ( 2418) Misc. bond : bond 0.57308 / 22.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.503 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.9101 time to fit residues: 200.5860 Evaluate side-chains 161 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 0.0040 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 429 ASN K 488 GLN K 491 ASN L 93 GLN D 46 HIS F 93 GLN H 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.125706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.090545 restraints weight = 23508.090| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.50 r_work: 0.3034 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17208 Z= 0.138 Angle : 0.655 9.607 24484 Z= 0.371 Chirality : 0.046 0.235 2772 Planarity : 0.004 0.040 2097 Dihedral : 28.988 169.221 4627 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.74 % Allowed : 9.70 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.24), residues: 1274 helix: 1.51 (0.18), residues: 790 sheet: -0.24 (0.68), residues: 75 loop : -1.99 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 30 TYR 0.013 0.001 TYR K 214 PHE 0.020 0.001 PHE K 409 TRP 0.012 0.002 TRP K 39 HIS 0.004 0.001 HIS K 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (17205) covalent geometry : angle 0.65490 / 0.37 (24484) hydrogen bonds : bond 0.05253 / 3.56 ( 945) hydrogen bonds : angle 3.47756 / 2.46 ( 2418) Misc. bond : bond 0.00464 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: K 275 GLU cc_start: 0.7989 (tt0) cc_final: 0.7342 (mp0) REVERT: K 398 ARG cc_start: 0.7783 (mmm160) cc_final: 0.7498 (mmm160) REVERT: K 401 GLU cc_start: 0.8391 (mp0) cc_final: 0.8158 (mp0) REVERT: C 92 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: D 76 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8410 (ptp90) outliers start: 19 outliers final: 6 residues processed: 188 average time/residue: 0.8119 time to fit residues: 164.0583 Evaluate side-chains 176 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 147 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 429 ASN K 447 ASN K 488 GLN D 46 HIS D 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.122459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.087061 restraints weight = 23677.241| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.47 r_work: 0.2965 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17208 Z= 0.234 Angle : 0.695 9.710 24484 Z= 0.383 Chirality : 0.049 0.227 2772 Planarity : 0.004 0.054 2097 Dihedral : 29.192 167.158 4627 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.29 % Allowed : 10.61 % Favored : 87.10 % 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: 0.60 (0.24), residues: 1274 helix: 1.61 (0.18), residues: 792 sheet: -0.48 (0.66), residues: 80 loop : -1.96 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 457 TYR 0.014 0.002 TYR L 51 PHE 0.029 0.002 PHE K 409 TRP 0.006 0.001 TRP K 56 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (17205) covalent geometry : angle 0.69512 / 0.38 (24484) hydrogen bonds : bond 0.06393 / 4.30 ( 945) hydrogen bonds : angle 3.38715 / 2.39 ( 2418) Misc. bond : bond 0.00575 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.481 Fit side-chains REVERT: K 275 GLU cc_start: 0.8003 (tt0) cc_final: 0.7383 (mp0) REVERT: K 374 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8244 (mm-40) REVERT: K 401 GLU cc_start: 0.8436 (mp0) cc_final: 0.8213 (mp0) REVERT: C 92 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8103 (mt-10) REVERT: D 44 GLN cc_start: 0.8903 (mt0) cc_final: 0.8630 (mt0) REVERT: D 76 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8445 (ptp90) outliers start: 25 outliers final: 11 residues processed: 183 average time/residue: 0.8303 time to fit residues: 163.0701 Evaluate side-chains 187 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 48 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.123388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.087831 restraints weight = 23569.214| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.51 r_work: 0.2983 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17208 Z= 0.158 Angle : 0.665 9.609 24484 Z= 0.369 Chirality : 0.047 0.226 2772 Planarity : 0.004 0.038 2097 Dihedral : 29.197 163.453 4627 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.20 % Allowed : 11.71 % Favored : 86.09 % 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: 0.78 (0.24), residues: 1274 helix: 1.73 (0.18), residues: 791 sheet: -0.41 (0.66), residues: 80 loop : -1.82 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.011 0.001 TYR L 51 PHE 0.024 0.001 PHE K 409 TRP 0.011 0.001 TRP K 39 HIS 0.003 0.001 HIS K 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (17205) covalent geometry : angle 0.66521 / 0.37 (24484) hydrogen bonds : bond 0.05600 / 3.79 ( 945) hydrogen bonds : angle 3.33538 / 2.36 ( 2418) Misc. bond : bond 0.00486 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.483 Fit side-chains REVERT: K 132 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: K 275 GLU cc_start: 0.7985 (tt0) cc_final: 0.7350 (mp0) REVERT: K 374 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8223 (mm-40) REVERT: K 401 GLU cc_start: 0.8423 (mp0) cc_final: 0.8169 (mp0) REVERT: L 24 ASP cc_start: 0.8311 (t70) cc_final: 0.7957 (t0) REVERT: C 64 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8390 (tp30) REVERT: C 92 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: D 76 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8360 (ptp90) REVERT: D 90 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: G 64 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8081 (tp30) REVERT: H 43 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8782 (mmtm) outliers start: 24 outliers final: 13 residues processed: 183 average time/residue: 0.8199 time to fit residues: 161.5512 Evaluate side-chains 194 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 chunk 75 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.124135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.088765 restraints weight = 23454.894| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.50 r_work: 0.3004 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17208 Z= 0.137 Angle : 0.655 9.282 24484 Z= 0.364 Chirality : 0.046 0.221 2772 Planarity : 0.004 0.053 2097 Dihedral : 29.183 163.361 4627 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.65 % Allowed : 12.90 % Favored : 85.45 % 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: 0.93 (0.24), residues: 1274 helix: 1.85 (0.18), residues: 791 sheet: -0.36 (0.65), residues: 80 loop : -1.75 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 89 TYR 0.012 0.001 TYR K 214 PHE 0.021 0.001 PHE K 409 TRP 0.017 0.002 TRP K 39 HIS 0.003 0.001 HIS L 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (17205) covalent geometry : angle 0.65457 / 0.36 (24484) hydrogen bonds : bond 0.05125 / 3.48 ( 945) hydrogen bonds : angle 3.28338 / 2.32 ( 2418) Misc. bond : bond 0.00188 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.494 Fit side-chains REVERT: K 275 GLU cc_start: 0.7974 (tt0) cc_final: 0.7306 (mp0) REVERT: K 374 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8243 (mm-40) REVERT: K 394 ASP cc_start: 0.8182 (t70) cc_final: 0.7878 (t0) REVERT: K 401 GLU cc_start: 0.8414 (mp0) cc_final: 0.8170 (mp0) REVERT: L 24 ASP cc_start: 0.8309 (t70) cc_final: 0.7959 (t0) REVERT: C 64 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8375 (tp30) REVERT: C 92 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: D 76 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8394 (ptp90) REVERT: D 90 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8197 (mp0) REVERT: G 64 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8063 (tp30) outliers start: 18 outliers final: 9 residues processed: 181 average time/residue: 0.8486 time to fit residues: 165.4117 Evaluate side-chains 188 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 44 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 122 optimal weight: 0.0020 chunk 61 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.122891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.087587 restraints weight = 23448.771| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.46 r_work: 0.2973 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17208 Z= 0.207 Angle : 0.673 9.493 24484 Z= 0.370 Chirality : 0.048 0.222 2772 Planarity : 0.004 0.050 2097 Dihedral : 29.230 162.624 4627 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.38 % Allowed : 12.72 % Favored : 84.90 % 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: 0.91 (0.24), residues: 1274 helix: 1.82 (0.18), residues: 791 sheet: -0.35 (0.65), residues: 80 loop : -1.75 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.012 0.001 TYR F 51 PHE 0.023 0.002 PHE K 409 TRP 0.016 0.002 TRP K 39 HIS 0.003 0.001 HIS K 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 (17205) covalent geometry : angle 0.67268 / 0.37 (24484) hydrogen bonds : bond 0.05821 / 3.94 ( 945) hydrogen bonds : angle 3.25917 / 2.31 ( 2418) Misc. bond : bond 0.00443 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.498 Fit side-chains REVERT: K 132 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8426 (mp0) REVERT: K 275 GLU cc_start: 0.7983 (tt0) cc_final: 0.7346 (mp0) REVERT: K 374 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8252 (mm-40) REVERT: K 394 ASP cc_start: 0.8148 (t70) cc_final: 0.7860 (t0) REVERT: K 401 GLU cc_start: 0.8433 (mp0) cc_final: 0.8201 (mp0) REVERT: C 64 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8341 (tp30) REVERT: C 92 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8077 (mt-10) REVERT: D 76 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8502 (ptp90) REVERT: G 64 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8108 (tp30) outliers start: 26 outliers final: 11 residues processed: 180 average time/residue: 0.8409 time to fit residues: 162.9130 Evaluate side-chains 186 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 132 GLU Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 131 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 114 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.123794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.088297 restraints weight = 23336.961| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.50 r_work: 0.2951 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17208 Z= 0.130 Angle : 0.654 9.133 24484 Z= 0.362 Chirality : 0.046 0.227 2772 Planarity : 0.004 0.038 2097 Dihedral : 29.228 161.656 4627 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.92 % Allowed : 14.00 % Favored : 84.08 % 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: 1.07 (0.24), residues: 1274 helix: 1.96 (0.18), residues: 790 sheet: -0.30 (0.65), residues: 80 loop : -1.70 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 454 TYR 0.012 0.001 TYR K 214 PHE 0.018 0.001 PHE K 409 TRP 0.017 0.001 TRP K 39 HIS 0.003 0.001 HIS L 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.13 (17205) covalent geometry : angle 0.65431 / 0.36 (24484) hydrogen bonds : bond 0.05274 / 3.58 ( 945) hydrogen bonds : angle 3.23685 / 2.29 ( 2418) Misc. bond : bond 0.00141 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.511 Fit side-chains REVERT: K 275 GLU cc_start: 0.7973 (tt0) cc_final: 0.7321 (mp0) REVERT: K 374 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8259 (mm-40) REVERT: K 401 GLU cc_start: 0.8446 (mp0) cc_final: 0.8188 (mp0) REVERT: A 133 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8510 (mt-10) REVERT: C 64 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8316 (tp30) REVERT: C 92 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: D 76 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8468 (ptp90) outliers start: 21 outliers final: 11 residues processed: 178 average time/residue: 0.8532 time to fit residues: 163.5738 Evaluate side-chains 184 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 9.9990 chunk 86 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.122606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.087294 restraints weight = 23381.971| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.45 r_work: 0.2972 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17208 Z= 0.215 Angle : 0.681 9.470 24484 Z= 0.373 Chirality : 0.048 0.225 2772 Planarity : 0.004 0.054 2097 Dihedral : 29.267 160.354 4627 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.74 % Allowed : 14.55 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.24), residues: 1274 helix: 1.91 (0.18), residues: 784 sheet: -0.32 (0.64), residues: 80 loop : -1.65 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 83 TYR 0.012 0.002 TYR F 51 PHE 0.022 0.002 PHE K 409 TRP 0.026 0.002 TRP K 39 HIS 0.003 0.001 HIS K 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (17205) covalent geometry : angle 0.68138 / 0.37 (24484) hydrogen bonds : bond 0.05915 / 4.00 ( 945) hydrogen bonds : angle 3.24075 / 2.30 ( 2418) Misc. bond : bond 0.00386 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: K 275 GLU cc_start: 0.7992 (tt0) cc_final: 0.7359 (mp0) REVERT: K 374 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8223 (mm-40) REVERT: K 401 GLU cc_start: 0.8427 (mp0) cc_final: 0.8214 (mp0) REVERT: A 133 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8514 (mt-10) REVERT: C 64 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8269 (tp30) REVERT: C 92 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8062 (mt-10) REVERT: G 64 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8111 (tp30) outliers start: 19 outliers final: 10 residues processed: 175 average time/residue: 0.8497 time to fit residues: 159.8935 Evaluate side-chains 181 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 99 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 137 optimal weight: 20.0000 chunk 125 optimal weight: 40.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 25 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.123413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.087945 restraints weight = 23400.861| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.49 r_work: 0.2945 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17208 Z= 0.138 Angle : 0.668 9.127 24484 Z= 0.368 Chirality : 0.046 0.227 2772 Planarity : 0.004 0.042 2097 Dihedral : 29.259 158.935 4627 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.83 % Allowed : 14.82 % Favored : 83.35 % 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: 1.13 (0.24), residues: 1274 helix: 2.01 (0.18), residues: 784 sheet: -0.30 (0.64), residues: 80 loop : -1.60 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG K 145 TYR 0.013 0.001 TYR K 214 PHE 0.042 0.002 PHE K 409 TRP 0.030 0.002 TRP K 39 HIS 0.003 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (17205) covalent geometry : angle 0.66833 / 0.37 (24484) hydrogen bonds : bond 0.05376 / 3.65 ( 945) hydrogen bonds : angle 3.22700 / 2.29 ( 2418) Misc. bond : bond 0.00149 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: K 275 GLU cc_start: 0.7969 (tt0) cc_final: 0.7283 (mp0) REVERT: K 374 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8249 (mm-40) REVERT: K 401 GLU cc_start: 0.8460 (mp0) cc_final: 0.8188 (mp0) REVERT: A 133 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8497 (mt-10) REVERT: C 64 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8226 (tp30) REVERT: C 92 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: F 93 GLN cc_start: 0.8483 (mt0) cc_final: 0.8260 (mm-40) outliers start: 20 outliers final: 11 residues processed: 173 average time/residue: 0.8031 time to fit residues: 149.8030 Evaluate side-chains 180 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain K residue 541 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 9 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 152 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.123437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.088021 restraints weight = 23309.019| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.49 r_work: 0.2945 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17208 Z= 0.173 Angle : 0.674 10.860 24484 Z= 0.368 Chirality : 0.047 0.224 2772 Planarity : 0.004 0.040 2097 Dihedral : 29.252 158.071 4627 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.46 % Allowed : 15.37 % Favored : 83.17 % 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: 1.11 (0.24), residues: 1274 helix: 1.97 (0.18), residues: 784 sheet: -0.26 (0.64), residues: 80 loop : -1.57 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 145 TYR 0.011 0.001 TYR F 51 PHE 0.012 0.001 PHE K 409 TRP 0.024 0.002 TRP K 39 HIS 0.003 0.001 HIS L 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (17205) covalent geometry : angle 0.67364 / 0.37 (24484) hydrogen bonds : bond 0.05333 / 3.62 ( 945) hydrogen bonds : angle 3.20614 / 2.27 ( 2418) Misc. bond : bond 0.00206 / 0.09 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: K 275 GLU cc_start: 0.7971 (tt0) cc_final: 0.7275 (mp0) REVERT: K 374 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8250 (mm-40) REVERT: K 401 GLU cc_start: 0.8468 (mp0) cc_final: 0.8204 (mp0) REVERT: A 133 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8490 (mt-10) REVERT: C 64 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8513 (tp30) REVERT: C 92 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8051 (mt-10) outliers start: 16 outliers final: 10 residues processed: 170 average time/residue: 0.8256 time to fit residues: 151.1132 Evaluate side-chains 178 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 374 GLN Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 474 THR Chi-restraints excluded: chain K residue 541 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 80 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** 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 = 0.3676 r_free = 0.3676 target = 0.122414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.087083 restraints weight = 23483.269| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.46 r_work: 0.2972 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17208 Z= 0.217 Angle : 0.700 11.605 24484 Z= 0.379 Chirality : 0.048 0.227 2772 Planarity : 0.004 0.052 2097 Dihedral : 29.294 152.654 4627 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.56 % Allowed : 15.10 % Favored : 83.35 % 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: 1.00 (0.24), residues: 1274 helix: 1.85 (0.18), residues: 790 sheet: -0.32 (0.64), residues: 80 loop : -1.59 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 145 TYR 0.013 0.002 TYR L 51 PHE 0.023 0.002 PHE K 409 TRP 0.021 0.002 TRP K 39 HIS 0.003 0.001 HIS K 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 (17205) covalent geometry : angle 0.69979 / 0.38 (24484) hydrogen bonds : bond 0.05995 / 4.05 ( 945) hydrogen bonds : angle 3.23389 / 2.29 ( 2418) Misc. bond : bond 0.00237 / 0.10 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6165.74 seconds wall clock time: 105 minutes 34.42 seconds (6334.42 seconds total)