Starting phenix.real_space_refine on Sat Jul 4 13:29:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9geq_51301/07_2026/9geq_51301.cif Found real_map, /net/cci-nas-00/data/ceres_data/9geq_51301/07_2026/9geq_51301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9geq_51301/07_2026/9geq_51301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9geq_51301/07_2026/9geq_51301.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9geq_51301/07_2026/9geq_51301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9geq_51301/07_2026/9geq_51301.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.264 sd= 1.103 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 2 7.16 5 P 266 5.49 5 S 76 5.16 5 Cl 2 4.86 5 C 12310 2.51 5 N 3844 2.21 5 O 4386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20888 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2743 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "J" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2710 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 837 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 10, 'TRANS': 93} Chain: "N" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3732 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 429} Chain: "K" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 837 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 10, 'TRANS': 93} Chain: "L" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3732 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 429} Chain: "O" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.68, per 1000 atoms: 0.18 Number of scatterers: 20888 At special positions: 0 Unit cell: (123.76, 125.8, 150.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 2 26.01 Ca 2 19.99 Cl 2 17.00 S 76 16.00 P 266 15.00 O 4386 8.00 N 3844 7.00 C 12310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS M 1 " - pdb=" SG CYS M 14 " distance=2.03 Simple disulfide: pdb=" SG CYS N 115 " - pdb=" SG CYS N 125 " distance=2.03 Simple disulfide: pdb=" SG CYS N 119 " - pdb=" SG CYS N 143 " distance=2.03 Simple disulfide: pdb=" SG CYS N 153 " - pdb=" SG CYS L 153 " distance=2.03 Simple disulfide: pdb=" SG CYS N 221 " - pdb=" SG CYS N 232 " distance=2.03 Simple disulfide: pdb=" SG CYS N 440 " - pdb=" SG CYS N 497 " distance=2.03 Simple disulfide: pdb=" SG CYS N 538 " - pdb=" SG CYS N 564 " distance=2.03 Simple disulfide: pdb=" SG CYS K 1 " - pdb=" SG CYS K 14 " distance=2.03 Simple disulfide: pdb=" SG CYS L 115 " - pdb=" SG CYS L 125 " distance=2.03 Simple disulfide: pdb=" SG CYS L 119 " - pdb=" SG CYS L 143 " distance=2.03 Simple disulfide: pdb=" SG CYS L 221 " - pdb=" SG CYS L 232 " distance=2.03 Simple disulfide: pdb=" SG CYS L 440 " - pdb=" SG CYS L 497 " distance=2.03 Simple disulfide: pdb=" SG CYS L 538 " - pdb=" SG CYS L 564 " distance=2.03 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=9, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 5 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " BETA1-6 " NAG O 1 " - " FUC O 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 6 " NAG-ASN " NAG L 601 " - " ASN L 189 " " NAG L 602 " - " ASN L 225 " " NAG N 601 " - " ASN N 189 " " NAG N 602 " - " ASN N 225 " " NAG O 1 " - " ASN N 317 " " NAG P 1 " - " ASN L 317 " Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 691.5 milliseconds 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3564 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 21 sheets defined 56.2% alpha, 3.4% beta 128 base pairs and 219 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 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: 3.833A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.509A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.707A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) 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: 3.667A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.036A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.515A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.796A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.509A 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 36 Processing helix chain 'G' and resid 46 through 73 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 removed outlier: 3.639A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) 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: 3.816A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 68 Processing helix chain 'M' and resid 72 through 76 Processing helix chain 'M' and resid 84 through 98 Processing helix chain 'N' and resid 173 through 178 removed outlier: 3.533A pdb=" N TYR N 177 " --> pdb=" O ALA N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 187 Processing helix chain 'N' and resid 219 through 225 removed outlier: 3.935A pdb=" N LEU N 223 " --> pdb=" O ASP N 219 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR N 224 " --> pdb=" O PRO N 220 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASN N 225 " --> pdb=" O CYS N 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 219 through 225' Processing helix chain 'N' and resid 243 through 268 Processing helix chain 'N' and resid 272 through 295 Processing helix chain 'N' and resid 295 through 302 removed outlier: 4.038A pdb=" N LEU N 299 " --> pdb=" O ASP N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 302 through 310 Processing helix chain 'N' and resid 325 through 332 removed outlier: 3.758A pdb=" N THR N 329 " --> pdb=" O ALA N 325 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN N 330 " --> pdb=" O ASN N 326 " (cutoff:3.500A) Processing helix chain 'N' and resid 333 through 338 Processing helix chain 'N' and resid 362 through 364 No H-bonds generated for 'chain 'N' and resid 362 through 364' Processing helix chain 'N' and resid 367 through 374 removed outlier: 3.890A pdb=" N VAL N 371 " --> pdb=" O ALA N 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 377 through 386 Processing helix chain 'N' and resid 400 through 405 Processing helix chain 'N' and resid 416 through 428 Processing helix chain 'N' and resid 432 through 440 Processing helix chain 'N' and resid 447 through 456 Processing helix chain 'N' and resid 457 through 469 Processing helix chain 'N' and resid 470 through 474 Processing helix chain 'N' and resid 475 through 483 Processing helix chain 'N' and resid 492 through 509 Processing helix chain 'N' and resid 521 through 529 Processing helix chain 'N' and resid 532 through 541 Processing helix chain 'N' and resid 565 through 567 No H-bonds generated for 'chain 'N' and resid 565 through 567' Processing helix chain 'N' and resid 572 through 576 Processing helix chain 'K' and resid 60 through 68 Processing helix chain 'K' and resid 72 through 76 Processing helix chain 'K' and resid 84 through 98 Processing helix chain 'L' and resid 173 through 178 Processing helix chain 'L' and resid 180 through 187 Processing helix chain 'L' and resid 220 through 225 removed outlier: 3.909A pdb=" N THR L 224 " --> pdb=" O PRO L 220 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN L 225 " --> pdb=" O CYS L 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 220 through 225' Processing helix chain 'L' and resid 243 through 268 Processing helix chain 'L' and resid 272 through 296 Processing helix chain 'L' and resid 296 through 302 Processing helix chain 'L' and resid 302 through 310 Processing helix chain 'L' and resid 327 through 332 Processing helix chain 'L' and resid 333 through 338 Processing helix chain 'L' and resid 362 through 364 No H-bonds generated for 'chain 'L' and resid 362 through 364' Processing helix chain 'L' and resid 368 through 374 Processing helix chain 'L' and resid 377 through 386 Processing helix chain 'L' and resid 399 through 405 Processing helix chain 'L' and resid 416 through 428 Processing helix chain 'L' and resid 432 through 440 Processing helix chain 'L' and resid 447 through 456 Processing helix chain 'L' and resid 457 through 469 Processing helix chain 'L' and resid 470 through 474 Processing helix chain 'L' and resid 475 through 483 Processing helix chain 'L' and resid 492 through 509 Processing helix chain 'L' and resid 521 through 529 Processing helix chain 'L' and resid 532 through 541 Processing helix chain 'L' and resid 565 through 567 No H-bonds generated for 'chain 'L' and resid 565 through 567' Processing helix chain 'L' and resid 571 through 576 removed outlier: 4.355A pdb=" N SER L 574 " --> pdb=" O ASN L 571 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.826A 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 96 through 98 removed outlier: 6.536A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.254A 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: 6.750A 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: 6.902A 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: 7.145A 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 'M' and resid 27 through 28 Processing sheet with id=AB3, first strand: chain 'M' and resid 52 through 53 Processing sheet with id=AB4, first strand: chain 'M' and resid 78 through 83 removed outlier: 4.238A pdb=" N ALA N 389 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 128 through 129 Processing sheet with id=AB6, first strand: chain 'N' and resid 342 through 344 Processing sheet with id=AB7, first strand: chain 'N' and resid 545 through 547 Processing sheet with id=AB8, first strand: chain 'K' and resid 27 through 28 Processing sheet with id=AB9, first strand: chain 'K' and resid 78 through 83 removed outlier: 3.979A pdb=" N ALA L 389 " --> pdb=" O ASP K 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 128 through 129 Processing sheet with id=AC2, first strand: chain 'L' and resid 342 through 344 Processing sheet with id=AC3, first strand: chain 'L' and resid 545 through 547 728 hydrogen bonds defined for protein. 2097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 326 hydrogen bonds 652 hydrogen bond angles 0 basepair planarities 128 basepair parallelities 219 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 8430 1.39 - 1.56: 12773 1.56 - 1.74: 530 1.74 - 1.91: 122 1.91 - 2.08: 8 Bond restraints: 21863 Sorted by residual: bond pdb=" C3' DA J 23 " pdb=" C2' DA J 23 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DT I -67 " pdb=" C2' DT I -67 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DA I -1 " pdb=" C2' DA I -1 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC I 1 " pdb=" C2' DC I 1 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DG J 52 " pdb=" C2' DG J 52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 ... (remaining 21858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 30624 3.04 - 6.08: 132 6.08 - 9.12: 8 9.12 - 12.16: 1 12.16 - 15.20: 1 Bond angle restraints: 30766 Sorted by residual: angle pdb=" O4' DA I -68 " pdb=" C1' DA I -68 " pdb=" N9 DA I -68 " ideal model delta sigma weight residual 108.00 111.51 -3.51 7.00e-01 2.04e+00 2.52e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT J 1 " pdb=" C4 DT J 1 " pdb=" O4 DT J 1 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I -67 " pdb=" C4 DT I -67 " pdb=" O4 DT I -67 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 30761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.15: 11121 34.15 - 68.29: 1604 68.29 - 102.44: 43 102.44 - 136.58: 1 136.58 - 170.73: 2 Dihedral angle restraints: 12771 sinusoidal: 7262 harmonic: 5509 Sorted by residual: dihedral pdb=" CA GLU L 242 " pdb=" C GLU L 242 " pdb=" N MET L 243 " pdb=" CA MET L 243 " ideal model delta harmonic sigma weight residual -180.00 -139.34 -40.66 0 5.00e+00 4.00e-02 6.61e+01 dihedral pdb=" CB CYS N 153 " pdb=" SG CYS N 153 " pdb=" SG CYS L 153 " pdb=" CB CYS L 153 " ideal model delta sinusoidal sigma weight residual -86.00 -146.37 60.37 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CA GLU N 242 " pdb=" C GLU N 242 " pdb=" N MET N 243 " pdb=" CA MET N 243 " ideal model delta harmonic sigma weight residual -180.00 -146.53 -33.47 0 5.00e+00 4.00e-02 4.48e+01 ... (remaining 12768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2833 0.052 - 0.104: 534 0.104 - 0.155: 78 0.155 - 0.207: 3 0.207 - 0.259: 4 Chirality restraints: 3452 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN N 317 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1 NAG N 601 " pdb=" ND2 ASN N 189 " pdb=" C2 NAG N 601 " pdb=" O5 NAG N 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.05 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3449 not shown) Planarity restraints: 3030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN N 317 " -0.039 2.00e-02 2.50e+03 3.70e-02 1.71e+01 pdb=" CG ASN N 317 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN N 317 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN N 317 " 0.047 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN L 317 " 0.038 2.00e-02 2.50e+03 3.50e-02 1.53e+01 pdb=" CG ASN L 317 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN L 317 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN L 317 " -0.045 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN N 225 " 0.023 2.00e-02 2.50e+03 2.10e-02 5.52e+00 pdb=" CG ASN N 225 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN N 225 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN N 225 " -0.015 2.00e-02 2.50e+03 pdb=" C1 NAG N 602 " 0.019 2.00e-02 2.50e+03 ... (remaining 3027 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 516 2.68 - 3.24: 18520 3.24 - 3.79: 36762 3.79 - 4.35: 48836 4.35 - 4.90: 75067 Nonbonded interactions: 179701 Sorted by model distance: nonbonded pdb=" O ILE N 537 " pdb=" OG1 THR N 541 " model vdw 2.127 3.040 nonbonded pdb=" O ILE L 537 " pdb=" OG1 THR L 541 " model vdw 2.153 3.040 nonbonded pdb=" OE1 GLU L 242 " pdb=" CMB HEM K 202 " model vdw 2.197 2.768 nonbonded pdb=" OH TYR N 433 " pdb=" OE2 GLU N 483 " model vdw 2.219 3.040 nonbonded pdb=" OE2 GLU M 38 " pdb=" OG1 THR M 48 " model vdw 2.230 3.040 ... (remaining 179696 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 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } 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: 4.810 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 19.290 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.199 21901 Z= 0.377 Angle : 0.690 15.202 30840 Z= 0.519 Chirality : 0.042 0.259 3452 Planarity : 0.004 0.063 3024 Dihedral : 23.891 170.729 9168 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.53 % Allowed : 23.30 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.92 (0.20), residues: 1873 helix: 2.15 (0.17), residues: 976 sheet: None (None), residues: 0 loop : 0.37 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 559 TYR 0.011 0.001 TYR H 37 PHE 0.012 0.001 PHE K 86 TRP 0.007 0.001 TRP L 436 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.38 (21863) covalent geometry : angle 0.66408 / 0.52 (30766) SS BOND : bond 0.00210 / 0.11 ( 13) SS BOND : angle 0.73490 / 0.65 ( 26) hydrogen bonds : bond 0.11648 / 7.72 ( 1054) hydrogen bonds : angle 5.00112 / 3.56 ( 2749) Misc. bond : bond 0.07488 / 5.46 ( 9) link_ALPHA1-3 : bond 0.01284 / 0.89 ( 2) link_ALPHA1-3 : angle 1.45367 / 1.07 ( 6) link_ALPHA1-6 : bond 0.00844 / 0.59 ( 2) link_ALPHA1-6 : angle 1.38505 / 1.07 ( 6) link_BETA1-4 : bond 0.00646 / 0.40 ( 4) link_BETA1-4 : angle 1.84157 / 1.03 ( 12) link_BETA1-6 : bond 0.00205 / 0.14 ( 2) link_BETA1-6 : angle 2.20598 / 1.36 ( 6) link_NAG-ASN : bond 0.01088 / 0.72 ( 6) link_NAG-ASN : angle 7.50349 / 4.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 243 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8659 (mptt) cc_final: 0.8115 (mmtm) REVERT: C 64 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: C 92 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8026 (mm-30) REVERT: F 92 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8131 (ttp80) REVERT: H 68 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: H 88 SER cc_start: 0.9013 (t) cc_final: 0.8796 (m) REVERT: N 539 ASP cc_start: 0.7963 (m-30) cc_final: 0.7613 (m-30) REVERT: N 572 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8857 (mt) REVERT: L 267 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8004 (mp) REVERT: L 446 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7432 (tm-30) outliers start: 25 outliers final: 16 residues processed: 257 average time/residue: 0.2120 time to fit residues: 75.4078 Evaluate side-chains 259 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 243 MET Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 572 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 267 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 446 GLU Chi-restraints excluded: chain L residue 497 CYS Chi-restraints excluded: chain L residue 541 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS E 68 GLN F 25 ASN G 104 GLN L 206 ASN ** L 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.112453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.084500 restraints weight = 31822.349| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.67 r_work: 0.2903 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.216 21901 Z= 0.219 Angle : 0.658 15.945 30840 Z= 0.345 Chirality : 0.046 0.249 3452 Planarity : 0.005 0.043 3024 Dihedral : 26.086 173.780 5407 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.43 % Allowed : 20.05 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.63 (0.20), residues: 1873 helix: 1.97 (0.17), residues: 988 sheet: None (None), residues: 0 loop : 0.12 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 559 TYR 0.014 0.002 TYR D 34 PHE 0.015 0.002 PHE K 86 TRP 0.010 0.001 TRP K 89 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (21863) covalent geometry : angle 0.64249 / 0.34 (30766) SS BOND : bond 0.00868 / 0.61 ( 13) SS BOND : angle 1.03979 / 0.86 ( 26) hydrogen bonds : bond 0.05110 / 3.47 ( 1054) hydrogen bonds : angle 4.03770 / 2.88 ( 2749) Misc. bond : bond 0.07674 / 5.78 ( 9) link_ALPHA1-3 : bond 0.00938 / 0.65 ( 2) link_ALPHA1-3 : angle 1.54410 / 1.11 ( 6) link_ALPHA1-6 : bond 0.00426 / 0.30 ( 2) link_ALPHA1-6 : angle 1.61505 / 1.25 ( 6) link_BETA1-4 : bond 0.00419 / 0.28 ( 4) link_BETA1-4 : angle 2.11475 / 1.30 ( 12) link_BETA1-6 : bond 0.00323 / 0.22 ( 2) link_BETA1-6 : angle 1.50164 / 0.96 ( 6) link_NAG-ASN : bond 0.00920 / 0.61 ( 6) link_NAG-ASN : angle 5.45642 / 3.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 236 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7516 (mtt) REVERT: G 15 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8405 (mttm) REVERT: N 219 ASP cc_start: 0.7648 (t70) cc_final: 0.7321 (t70) REVERT: N 237 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7872 (t0) REVERT: N 256 GLU cc_start: 0.8398 (tp30) cc_final: 0.8145 (tp30) REVERT: N 539 ASP cc_start: 0.7966 (m-30) cc_final: 0.7589 (m-30) REVERT: L 175 MET cc_start: 0.8962 (pmt) cc_final: 0.8643 (pmt) REVERT: L 254 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8701 (tp) REVERT: L 446 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7695 (tm-30) outliers start: 56 outliers final: 37 residues processed: 273 average time/residue: 0.2064 time to fit residues: 78.4715 Evaluate side-chains 276 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 237 ASP Chi-restraints excluded: chain N residue 243 MET Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 447 THR Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 465 MET Chi-restraints excluded: chain N residue 497 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 446 GLU Chi-restraints excluded: chain L residue 497 CYS Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 566 THR Chi-restraints excluded: chain L residue 574 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 48 optimal weight: 0.5980 chunk 133 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 117 optimal weight: 0.0270 chunk 63 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN G 104 GLN H 106 HIS L 206 ASN ** L 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 526 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.086762 restraints weight = 31619.839| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.63 r_work: 0.2948 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.183 21901 Z= 0.123 Angle : 0.587 15.414 30840 Z= 0.312 Chirality : 0.042 0.371 3452 Planarity : 0.004 0.050 3024 Dihedral : 26.195 175.141 5379 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.64 % Allowed : 20.91 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.93 (0.20), residues: 1873 helix: 2.25 (0.17), residues: 987 sheet: None (None), residues: 0 loop : 0.23 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 349 TYR 0.010 0.001 TYR H 37 PHE 0.013 0.001 PHE K 86 TRP 0.008 0.001 TRP N 436 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (21863) covalent geometry : angle 0.57668 / 0.31 (30766) SS BOND : bond 0.00838 / 0.61 ( 13) SS BOND : angle 0.65323 / 0.57 ( 26) hydrogen bonds : bond 0.04207 / 2.85 ( 1054) hydrogen bonds : angle 3.74371 / 2.67 ( 2749) Misc. bond : bond 0.07054 / 5.08 ( 9) link_ALPHA1-3 : bond 0.01150 / 0.80 ( 2) link_ALPHA1-3 : angle 1.61013 / 1.20 ( 6) link_ALPHA1-6 : bond 0.00750 / 0.52 ( 2) link_ALPHA1-6 : angle 1.49640 / 1.17 ( 6) link_BETA1-4 : bond 0.00331 / 0.21 ( 4) link_BETA1-4 : angle 1.95968 / 1.19 ( 12) link_BETA1-6 : bond 0.00032 / 0.02 ( 2) link_BETA1-6 : angle 1.46793 / 0.93 ( 6) link_NAG-ASN : bond 0.00872 / 0.58 ( 6) link_NAG-ASN : angle 4.14503 / 2.56 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 25 ASN cc_start: 0.8791 (m110) cc_final: 0.8541 (m-40) REVERT: G 15 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8388 (mttm) REVERT: N 219 ASP cc_start: 0.7620 (t70) cc_final: 0.7245 (t70) REVERT: N 358 ARG cc_start: 0.8242 (mtp-110) cc_final: 0.7318 (ttp80) REVERT: N 459 LYS cc_start: 0.8659 (mttm) cc_final: 0.8453 (mmtm) REVERT: N 539 ASP cc_start: 0.7886 (m-30) cc_final: 0.7524 (m-30) REVERT: L 175 MET cc_start: 0.8898 (pmt) cc_final: 0.8465 (pmt) REVERT: L 254 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8693 (tp) REVERT: L 446 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: L 490 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8090 (mmt180) outliers start: 43 outliers final: 24 residues processed: 271 average time/residue: 0.2032 time to fit residues: 76.5243 Evaluate side-chains 261 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 497 CYS Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 577 GLU Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 446 GLU Chi-restraints excluded: chain L residue 490 ARG Chi-restraints excluded: chain L residue 497 CYS Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 574 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 149 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 30.0000 chunk 191 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 25 optimal weight: 0.0370 chunk 75 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN L 206 ASN ** L 421 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 = 0.3556 r_free = 0.3556 target = 0.114206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.086626 restraints weight = 31597.192| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.63 r_work: 0.2950 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.176 21901 Z= 0.131 Angle : 0.584 14.688 30840 Z= 0.309 Chirality : 0.042 0.251 3452 Planarity : 0.004 0.045 3024 Dihedral : 26.266 174.159 5376 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.76 % Allowed : 20.17 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.00 (0.20), residues: 1873 helix: 2.33 (0.17), residues: 986 sheet: None (None), residues: 0 loop : 0.23 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 349 TYR 0.010 0.001 TYR D 34 PHE 0.011 0.001 PHE K 86 TRP 0.007 0.001 TRP N 436 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (21863) covalent geometry : angle 0.57069 / 0.31 (30766) SS BOND : bond 0.00309 / 0.13 ( 13) SS BOND : angle 0.82026 / 0.73 ( 26) hydrogen bonds : bond 0.04148 / 2.82 ( 1054) hydrogen bonds : angle 3.65304 / 2.60 ( 2749) Misc. bond : bond 0.06534 / 4.81 ( 9) link_ALPHA1-3 : bond 0.01121 / 0.78 ( 2) link_ALPHA1-3 : angle 1.61416 / 1.19 ( 6) link_ALPHA1-6 : bond 0.00687 / 0.48 ( 2) link_ALPHA1-6 : angle 1.50024 / 1.17 ( 6) link_BETA1-4 : bond 0.00341 / 0.21 ( 4) link_BETA1-4 : angle 1.89496 / 1.21 ( 12) link_BETA1-6 : bond 0.00052 / 0.04 ( 2) link_BETA1-6 : angle 1.50764 / 1.00 ( 6) link_NAG-ASN : bond 0.01048 / 0.72 ( 6) link_NAG-ASN : angle 4.73191 / 2.84 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8192 (ttp80) REVERT: F 93 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8170 (mp10) REVERT: G 15 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8366 (mttm) REVERT: N 121 GLN cc_start: 0.8018 (tt0) cc_final: 0.7771 (tt0) REVERT: N 219 ASP cc_start: 0.7637 (t70) cc_final: 0.7237 (t70) REVERT: N 223 LEU cc_start: 0.8448 (mp) cc_final: 0.8131 (mp) REVERT: N 237 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7827 (t0) REVERT: N 265 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8115 (tptp) REVERT: N 539 ASP cc_start: 0.7873 (m-30) cc_final: 0.7522 (m-30) REVERT: N 562 VAL cc_start: 0.8090 (m) cc_final: 0.7877 (p) REVERT: K 52 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8784 (mttp) REVERT: L 175 MET cc_start: 0.8907 (pmt) cc_final: 0.8491 (pmt) REVERT: L 254 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8682 (tp) REVERT: L 267 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8116 (mp) REVERT: L 446 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8011 (tp30) REVERT: L 490 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8081 (mmt180) outliers start: 45 outliers final: 29 residues processed: 270 average time/residue: 0.2084 time to fit residues: 78.3610 Evaluate side-chains 269 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 237 ASP Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 265 LYS Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 497 CYS Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 577 GLU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 267 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 330 ASN Chi-restraints excluded: chain L residue 446 GLU Chi-restraints excluded: chain L residue 490 ARG Chi-restraints excluded: chain L residue 497 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 121 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 110 optimal weight: 0.4980 chunk 191 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN L 206 ASN ** L 421 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 = 0.3553 r_free = 0.3553 target = 0.113954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.086377 restraints weight = 31632.173| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.64 r_work: 0.2945 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.178 21901 Z= 0.137 Angle : 0.585 15.227 30840 Z= 0.308 Chirality : 0.042 0.242 3452 Planarity : 0.004 0.050 3024 Dihedral : 26.372 174.365 5376 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.43 % Allowed : 19.44 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2.00 (0.20), residues: 1873 helix: 2.32 (0.17), residues: 987 sheet: None (None), residues: 0 loop : 0.23 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 349 TYR 0.010 0.001 TYR D 34 PHE 0.012 0.001 PHE N 342 TRP 0.007 0.001 TRP N 436 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (21863) covalent geometry : angle 0.57363 / 0.31 (30766) SS BOND : bond 0.00263 / 0.12 ( 13) SS BOND : angle 0.77240 / 0.67 ( 26) hydrogen bonds : bond 0.04124 / 2.81 ( 1054) hydrogen bonds : angle 3.59878 / 2.56 ( 2749) Misc. bond : bond 0.06518 / 4.82 ( 9) link_ALPHA1-3 : bond 0.01128 / 0.78 ( 2) link_ALPHA1-3 : angle 1.64256 / 1.22 ( 6) link_ALPHA1-6 : bond 0.00683 / 0.47 ( 2) link_ALPHA1-6 : angle 1.49126 / 1.15 ( 6) link_BETA1-4 : bond 0.00269 / 0.16 ( 4) link_BETA1-4 : angle 1.98911 / 1.25 ( 12) link_BETA1-6 : bond 0.00127 / 0.09 ( 2) link_BETA1-6 : angle 1.55410 / 0.98 ( 6) link_NAG-ASN : bond 0.00904 / 0.62 ( 6) link_NAG-ASN : angle 4.24333 / 2.64 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 237 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8193 (ttp80) REVERT: F 93 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8186 (mp10) REVERT: G 15 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8381 (mttm) REVERT: H 83 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8031 (mtt-85) REVERT: N 121 GLN cc_start: 0.8040 (tt0) cc_final: 0.7827 (tt0) REVERT: N 219 ASP cc_start: 0.7623 (t70) cc_final: 0.7182 (t70) REVERT: N 223 LEU cc_start: 0.8406 (mp) cc_final: 0.8099 (mp) REVERT: N 237 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7818 (t0) REVERT: N 265 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8105 (tptp) REVERT: N 400 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8259 (t0) REVERT: N 539 ASP cc_start: 0.7846 (m-30) cc_final: 0.7457 (m-30) REVERT: K 52 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8801 (mttp) REVERT: L 254 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8682 (tp) REVERT: L 267 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8138 (mp) REVERT: L 446 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.8031 (tp30) REVERT: L 490 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8133 (mmt90) outliers start: 56 outliers final: 40 residues processed: 275 average time/residue: 0.2133 time to fit residues: 82.1215 Evaluate side-chains 283 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 237 ASP Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 265 LYS Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 447 THR Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 485 LEU Chi-restraints excluded: chain N residue 497 CYS Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 577 GLU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 267 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 330 ASN Chi-restraints excluded: chain L residue 446 GLU Chi-restraints excluded: chain L residue 490 ARG Chi-restraints excluded: chain L residue 497 CYS Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 566 THR Chi-restraints excluded: chain L residue 574 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 25 optimal weight: 0.0770 chunk 16 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 72 optimal weight: 30.0000 chunk 85 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN G 104 GLN L 206 ASN ** L 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 526 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.082585 restraints weight = 31686.924| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.63 r_work: 0.2883 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.207 21901 Z= 0.249 Angle : 0.675 16.574 30840 Z= 0.345 Chirality : 0.046 0.251 3452 Planarity : 0.005 0.045 3024 Dihedral : 26.674 179.526 5376 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.99 % Allowed : 18.82 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.56 (0.20), residues: 1873 helix: 1.96 (0.17), residues: 987 sheet: None (None), residues: 0 loop : 0.03 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 349 TYR 0.015 0.002 TYR D 34 PHE 0.017 0.002 PHE N 561 TRP 0.010 0.001 TRP K 89 HIS 0.005 0.001 HIS N 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 (21863) covalent geometry : angle 0.66290 / 0.34 (30766) SS BOND : bond 0.00594 / 0.36 ( 13) SS BOND : angle 1.10307 / 0.92 ( 26) hydrogen bonds : bond 0.05285 / 3.59 ( 1054) hydrogen bonds : angle 3.84108 / 2.74 ( 2749) Misc. bond : bond 0.07165 / 5.47 ( 9) link_ALPHA1-3 : bond 0.00902 / 0.63 ( 2) link_ALPHA1-3 : angle 1.70804 / 1.25 ( 6) link_ALPHA1-6 : bond 0.00182 / 0.13 ( 2) link_ALPHA1-6 : angle 1.83499 / 1.44 ( 6) link_BETA1-4 : bond 0.00263 / 0.16 ( 4) link_BETA1-4 : angle 2.37152 / 1.47 ( 12) link_BETA1-6 : bond 0.00349 / 0.25 ( 2) link_BETA1-6 : angle 1.60128 / 0.95 ( 6) link_NAG-ASN : bond 0.00870 / 0.56 ( 6) link_NAG-ASN : angle 4.54956 / 2.86 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 224 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9271 (mtmp) cc_final: 0.9041 (mtmt) REVERT: E 120 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8003 (mtt) REVERT: F 92 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8019 (ttp80) REVERT: F 93 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8201 (mp10) REVERT: G 15 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8439 (mttm) REVERT: H 83 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8095 (mtt-85) REVERT: N 219 ASP cc_start: 0.7712 (t70) cc_final: 0.7376 (t70) REVERT: N 237 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7915 (t0) REVERT: N 265 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8174 (tptp) REVERT: N 400 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8341 (t0) REVERT: N 539 ASP cc_start: 0.7919 (m-30) cc_final: 0.7503 (m-30) REVERT: K 52 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8827 (mttp) REVERT: L 254 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8667 (tp) REVERT: L 446 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8062 (tp30) REVERT: L 490 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8023 (mmt90) outliers start: 65 outliers final: 40 residues processed: 265 average time/residue: 0.2132 time to fit residues: 78.8184 Evaluate side-chains 274 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 223 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 237 ASP Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 265 LYS Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 447 THR Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 465 MET Chi-restraints excluded: chain N residue 497 CYS Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 330 ASN Chi-restraints excluded: chain L residue 446 GLU Chi-restraints excluded: chain L residue 490 ARG Chi-restraints excluded: chain L residue 497 CYS Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 566 THR Chi-restraints excluded: chain L residue 574 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.1507 > 50: distance: 28 - 34: 34.108 distance: 34 - 35: 57.713 distance: 35 - 36: 60.559 distance: 36 - 37: 17.323 distance: 36 - 38: 20.923 distance: 38 - 39: 39.439 distance: 39 - 40: 14.325 distance: 40 - 41: 24.790 distance: 40 - 49: 45.871 distance: 42 - 43: 21.561 distance: 43 - 44: 44.261 distance: 43 - 45: 45.421 distance: 44 - 46: 48.966 distance: 45 - 47: 41.335 distance: 46 - 48: 41.584 distance: 47 - 48: 57.134 distance: 49 - 50: 42.243 distance: 50 - 51: 48.910 distance: 50 - 53: 10.112 distance: 51 - 52: 13.712 distance: 53 - 54: 39.927 distance: 55 - 56: 39.700 distance: 56 - 59: 41.029 distance: 57 - 58: 69.880 distance: 57 - 63: 40.642 distance: 59 - 60: 41.077 distance: 60 - 61: 57.822 distance: 60 - 62: 68.632 distance: 63 - 64: 67.609 distance: 63 - 69: 39.704 distance: 64 - 65: 37.797 distance: 64 - 67: 38.724 distance: 65 - 70: 68.796 distance: 67 - 68: 41.305 distance: 71 - 72: 55.762 distance: 71 - 74: 39.984 distance: 72 - 73: 39.948 distance: 72 - 82: 40.512 distance: 74 - 75: 69.453 distance: 75 - 76: 68.988 distance: 75 - 77: 56.053 distance: 76 - 78: 59.115 distance: 77 - 79: 32.100 distance: 78 - 80: 43.486 distance: 79 - 80: 38.425 distance: 80 - 81: 55.851 distance: 82 - 83: 38.764 distance: 84 - 86: 38.979 distance: 86 - 87: 38.876 distance: 87 - 88: 69.346 distance: 87 - 90: 56.857 distance: 88 - 89: 40.362 distance: 88 - 100: 69.255 distance: 90 - 91: 39.041 distance: 91 - 92: 38.807 distance: 91 - 93: 3.930 distance: 93 - 95: 10.025 distance: 93 - 96: 33.253 distance: 94 - 95: 28.754 distance: 95 - 97: 38.270 distance: 96 - 98: 20.115 distance: 98 - 99: 46.799 distance: 101 - 102: 47.055 distance: 102 - 103: 43.030 distance: 102 - 107: 43.057 distance: 104 - 105: 39.345 distance: 107 - 108: 30.415 distance: 107 - 113: 41.208 distance: 108 - 111: 56.976 distance: 109 - 114: 35.208 distance: 111 - 112: 23.230 distance: 112 - 113: 21.690