Starting phenix.real_space_refine on Sun Jul 5 04:14:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ihf_52870/07_2026/9ihf_52870.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ihf_52870/07_2026/9ihf_52870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ihf_52870/07_2026/9ihf_52870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ihf_52870/07_2026/9ihf_52870.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ihf_52870/07_2026/9ihf_52870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ihf_52870/07_2026/9ihf_52870.map" } resolution = 3.16 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= 0.342 sd= 1.208 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: 6 Type Number sf(0) Gaussians Fe 3 7.16 5 P 266 5.49 5 S 99 5.16 5 C 15061 2.51 5 N 4632 2.21 5 O 5152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s 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: 25213 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} 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: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} 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: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 806 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "L" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3670 Classifications: {'peptide': 457} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 420} Chain: "M" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 806 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "N" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3670 Classifications: {'peptide': 457} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 420} Chain: "O" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 806 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "P" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3670 Classifications: {'peptide': 457} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 420} Chain: "Q" 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: "R" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Unusual residues: {'HEM': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'HEM': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'HEM': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.46, per 1000 atoms: 0.26 Number of scatterers: 25213 At special positions: 0 Unit cell: (138.04, 123.08, 169.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 3 26.01 S 99 16.00 P 266 15.00 O 5152 8.00 N 4632 7.00 C 15061 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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 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 P 221 " - pdb=" SG CYS P 232 " 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=3, symmetry=0 Links applied ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " ALPHA1-6 " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 4 " BETA1-4 " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " BETA1-6 " NAG Q 1 " - " FUC Q 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG R 1 " - " FUC R 5 " NAG-ASN " NAG L 603 " - " ASN L 189 " " NAG L 604 " - " ASN L 317 " " NAG N 603 " - " ASN N 189 " " NAG Q 1 " - " ASN N 317 " " NAG R 1 " - " ASN P 317 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 963.6 milliseconds 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4550 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 23 sheets defined 53.6% alpha, 2.7% beta 123 base pairs and 225 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.083A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.506A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.622A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.546A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.609A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 35 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: 3.564A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 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: 3.875A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.935A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.568A 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 removed outlier: 3.504A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) 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 'H' and resid 35 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.743A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) 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 221 through 225 removed outlier: 3.852A pdb=" N THR L 224 " --> pdb=" O CYS L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 268 Processing helix chain 'L' and resid 272 through 302 removed outlier: 5.539A pdb=" N LEU L 297 " --> pdb=" O TYR L 293 " (cutoff:3.500A) Proline residue: L 298 - end of helix 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 373 Processing helix chain 'L' and resid 377 through 386 Processing helix chain 'L' and resid 400 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 458 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 540 Processing helix chain 'L' and resid 572 through 576 removed outlier: 3.974A pdb=" N ARG L 576 " --> pdb=" O ALA L 573 " (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: 3.798A 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 220 through 225 removed outlier: 3.711A pdb=" N THR N 224 " --> pdb=" O PRO N 220 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN N 225 " --> pdb=" O CYS N 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 220 through 225' Processing helix chain 'N' and resid 243 through 268 Processing helix chain 'N' and resid 272 through 302 removed outlier: 5.439A pdb=" N LEU N 297 " --> pdb=" O TYR N 293 " (cutoff:3.500A) Proline residue: N 298 - end of helix Processing helix chain 'N' and resid 302 through 310 Processing helix chain 'N' and resid 327 through 332 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 368 through 373 removed outlier: 3.510A pdb=" N VAL N 372 " --> pdb=" O SER N 368 " (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 removed outlier: 3.790A pdb=" N ALA N 461 " --> pdb=" O ASN N 457 " (cutoff:3.500A) Processing helix chain 'N' and resid 470 through 474 Processing helix chain 'N' and resid 475 through 483 removed outlier: 3.532A pdb=" N GLU N 483 " --> pdb=" O GLY N 479 " (cutoff:3.500A) 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 540 removed outlier: 3.501A pdb=" N ASN N 540 " --> pdb=" O ILE N 536 " (cutoff:3.500A) Processing helix chain 'N' and resid 572 through 576 removed outlier: 3.794A pdb=" N ARG N 576 " --> pdb=" O ALA N 573 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 68 Processing helix chain 'O' and resid 72 through 76 Processing helix chain 'O' and resid 83 through 98 removed outlier: 3.965A pdb=" N MET O 87 " --> pdb=" O SER O 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 178 removed outlier: 3.665A pdb=" N TYR P 177 " --> pdb=" O ALA P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 188 Processing helix chain 'P' and resid 219 through 225 removed outlier: 3.749A pdb=" N ASN P 225 " --> pdb=" O CYS P 221 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 268 Processing helix chain 'P' and resid 272 through 302 removed outlier: 5.449A pdb=" N LEU P 297 " --> pdb=" O TYR P 293 " (cutoff:3.500A) Proline residue: P 298 - end of helix Processing helix chain 'P' and resid 302 through 310 Processing helix chain 'P' and resid 327 through 332 Processing helix chain 'P' and resid 333 through 339 removed outlier: 3.932A pdb=" N ILE P 339 " --> pdb=" O HIS P 336 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 364 No H-bonds generated for 'chain 'P' and resid 362 through 364' Processing helix chain 'P' and resid 368 through 373 removed outlier: 3.595A pdb=" N VAL P 372 " --> pdb=" O SER P 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 377 through 386 Processing helix chain 'P' and resid 399 through 405 Processing helix chain 'P' and resid 416 through 428 Processing helix chain 'P' and resid 432 through 440 Processing helix chain 'P' and resid 447 through 456 Processing helix chain 'P' and resid 458 through 469 Processing helix chain 'P' and resid 470 through 474 Processing helix chain 'P' and resid 475 through 483 Processing helix chain 'P' and resid 492 through 509 Processing helix chain 'P' and resid 521 through 529 Processing helix chain 'P' and resid 532 through 541 Processing helix chain 'P' and resid 572 through 576 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.072A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.187A 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: 6.685A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.284A 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: 7.352A 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 'K' and resid 27 through 28 removed outlier: 3.513A pdb=" N ARG K 27 " --> pdb=" O ASN L 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 Processing sheet with id=AB3, first strand: chain 'K' and resid 78 through 83 removed outlier: 4.230A pdb=" N ALA L 389 " --> pdb=" O ASP K 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 188 through 189 removed outlier: 4.447A pdb=" N LEU L 196 " --> pdb=" O ASN L 189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 342 through 344 Processing sheet with id=AB6, first strand: chain 'L' and resid 546 through 547 Processing sheet with id=AB7, first strand: chain 'M' and resid 27 through 28 Processing sheet with id=AB8, first strand: chain 'M' and resid 78 through 83 removed outlier: 4.040A pdb=" N ALA N 389 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 342 through 344 Processing sheet with id=AC1, first strand: chain 'N' and resid 546 through 547 Processing sheet with id=AC2, first strand: chain 'O' and resid 27 through 28 Processing sheet with id=AC3, first strand: chain 'O' and resid 52 through 53 Processing sheet with id=AC4, first strand: chain 'P' and resid 342 through 344 Processing sheet with id=AC5, first strand: chain 'P' and resid 546 through 547 869 hydrogen bonds defined for protein. 2499 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 315 hydrogen bonds 630 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 225 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 9961 1.38 - 1.55: 15637 1.55 - 1.72: 531 1.72 - 1.89: 163 1.89 - 2.06: 12 Bond restraints: 26304 Sorted by residual: bond pdb=" C1' DC J 35 " pdb=" N1 DC J 35 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.52e+01 bond pdb=" C3' DA I -30 " pdb=" C2' DA I -30 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.37e+01 bond pdb=" C3' DC I -40 " pdb=" C2' DC I -40 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.20e+00 bond pdb=" C3' DA J -31 " pdb=" C2' DA J -31 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.03e+00 bond pdb=" C3' DA I -68 " pdb=" C2' DA I -68 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.93e+00 ... (remaining 26299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 35976 2.03 - 4.05: 781 4.05 - 6.08: 43 6.08 - 8.10: 2 8.10 - 10.13: 3 Bond angle restraints: 36805 Sorted by residual: angle pdb=" N3 DT J 1 " pdb=" C4 DT J 1 " pdb=" O4 DT J 1 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J 30 " pdb=" C4 DT J 30 " pdb=" O4 DT J 30 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I -32 " pdb=" C4 DT I -32 " pdb=" O4 DT I -32 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 36800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 13648 33.77 - 67.53: 1732 67.53 - 101.30: 58 101.30 - 135.06: 14 135.06 - 168.83: 7 Dihedral angle restraints: 15459 sinusoidal: 8424 harmonic: 7035 Sorted by residual: dihedral pdb=" CB CYS L 221 " pdb=" SG CYS L 221 " pdb=" SG CYS L 232 " pdb=" CB CYS L 232 " ideal model delta sinusoidal sigma weight residual -86.00 -172.35 86.35 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CA TYR P 316 " pdb=" C TYR P 316 " pdb=" N ASN P 317 " pdb=" CA ASN P 317 " ideal model delta harmonic sigma weight residual 180.00 155.19 24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA CYS L 232 " pdb=" C CYS L 232 " pdb=" N PHE L 233 " pdb=" CA PHE L 233 " ideal model delta harmonic sigma weight residual -180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 15456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3765 0.075 - 0.150: 316 0.150 - 0.225: 5 0.225 - 0.300: 0 0.300 - 0.375: 2 Chirality restraints: 4088 Sorted by residual: chirality pdb=" C1 NAG L 603 " pdb=" ND2 ASN L 189 " pdb=" C2 NAG L 603 " pdb=" O5 NAG L 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN P 317 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ASN L 189 " pdb=" N ASN L 189 " pdb=" C ASN L 189 " pdb=" CB ASN L 189 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 4085 not shown) Planarity restraints: 3823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN P 317 " 0.042 2.00e-02 2.50e+03 3.91e-02 1.92e+01 pdb=" CG ASN P 317 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN P 317 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN P 317 " -0.048 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 110 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C GLU H 110 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU H 110 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY H 111 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 111 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.48e+00 pdb=" C GLY H 111 " -0.027 2.00e-02 2.50e+03 pdb=" O GLY H 111 " 0.010 2.00e-02 2.50e+03 pdb=" N THR H 112 " 0.009 2.00e-02 2.50e+03 ... (remaining 3820 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1821 2.74 - 3.28: 23002 3.28 - 3.82: 44831 3.82 - 4.36: 53409 4.36 - 4.90: 86591 Nonbonded interactions: 209654 Sorted by model distance: nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.195 3.120 nonbonded pdb=" OH TYR L 350 " pdb=" O THR L 545 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.261 3.040 nonbonded pdb=" NH1 ARG M 62 " pdb=" OD2 ASP N 416 " model vdw 2.264 3.120 nonbonded pdb=" N GLU N 517 " pdb=" OE1 GLU N 517 " model vdw 2.270 3.120 ... (remaining 209649 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 133) selection = (chain 'E' and resid 40 through 133) } 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' selection = chain 'O' } ncs_group { reference = (chain 'L' and resid 121 through 603) selection = chain 'N' 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: 5.850 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: 0.040 Extract box with map and model: 0.640 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.730 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 0.209 26327 Z= 0.343 Angle : 0.623 14.080 36859 Z= 0.474 Chirality : 0.041 0.375 4088 Planarity : 0.004 0.050 3818 Dihedral : 23.766 168.828 10891 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.58 % Allowed : 23.23 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % 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 (0.18), residues: 2396 helix: 2.12 (0.16), residues: 1161 sheet: -0.82 (0.85), residues: 36 loop : 0.05 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG P 456 TYR 0.009 0.001 TYR H 37 PHE 0.009 0.001 PHE O 86 TRP 0.008 0.001 TRP K 89 HIS 0.002 0.000 HIS P 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.34 (26304) covalent geometry : angle 0.61115 / 0.47 (36805) SS BOND : bond 0.00245 / 0.14 ( 6) SS BOND : angle 0.97939 / 0.55 ( 12) hydrogen bonds : bond 0.12663 / 8.41 ( 1184) hydrogen bonds : angle 5.18157 / 3.63 ( 3129) Misc. bond : bond 0.14680 / 7.57 ( 3) link_ALPHA1-3 : bond 0.00618 / 0.33 ( 1) link_ALPHA1-3 : angle 1.70258 / 0.96 ( 3) link_ALPHA1-6 : bond 0.00607 / 0.30 ( 2) link_ALPHA1-6 : angle 1.55582 / 0.75 ( 6) link_BETA1-4 : bond 0.00657 / 0.32 ( 4) link_BETA1-4 : angle 2.28799 / 1.41 ( 12) link_BETA1-6 : bond 0.00434 / 0.21 ( 2) link_BETA1-6 : angle 1.72761 / 1.00 ( 6) link_NAG-ASN : bond 0.00464 / 0.24 ( 5) link_NAG-ASN : angle 5.53897 / 2.97 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 276 time to evaluate : 0.827 Fit side-chains REVERT: A 42 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7716 (mmm-85) REVERT: A 56 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8090 (mtpp) REVERT: B 27 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8688 (mp10) REVERT: C 73 ASN cc_start: 0.8280 (t0) cc_final: 0.7977 (t0) REVERT: G 15 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8495 (pttp) REVERT: K 41 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: L 263 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8127 (tt0) REVERT: L 312 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8442 (m) REVERT: L 537 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.9065 (tt) REVERT: N 447 THR cc_start: 0.8881 (p) cc_final: 0.8559 (t) REVERT: O 38 GLU cc_start: 0.8625 (tt0) cc_final: 0.8224 (tt0) REVERT: O 48 THR cc_start: 0.9172 (m) cc_final: 0.8832 (p) REVERT: O 52 LYS cc_start: 0.8829 (mtmp) cc_final: 0.8503 (mttp) REVERT: O 67 GLU cc_start: 0.8603 (mp0) cc_final: 0.8125 (mp0) REVERT: O 70 ARG cc_start: 0.8833 (ttp80) cc_final: 0.8544 (ttt90) REVERT: O 80 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8377 (mp10) REVERT: P 169 SER cc_start: 0.8762 (m) cc_final: 0.8378 (p) REVERT: P 214 ASP cc_start: 0.7969 (t0) cc_final: 0.7702 (t0) REVERT: P 401 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8275 (mm-30) REVERT: P 446 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8371 (mp0) outliers start: 33 outliers final: 28 residues processed: 301 average time/residue: 0.2152 time to fit residues: 94.8531 Evaluate side-chains 304 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 41 PHE Chi-restraints excluded: chain L residue 140 GLN Chi-restraints excluded: chain L residue 221 CYS Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 537 ILE Chi-restraints excluded: chain L residue 543 ILE Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 149 SER Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 248 SER Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 540 ASN Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain P residue 174 SER Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 210 LEU Chi-restraints excluded: chain P residue 272 ASP Chi-restraints excluded: chain P residue 401 GLU Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.0670 chunk 111 optimal weight: 10.0000 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN F 25 ASN K 26 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 326 ASN M 54 ASN O 54 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.098779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.075414 restraints weight = 51776.588| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.81 r_work: 0.2944 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.0495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.266 26327 Z= 0.131 Angle : 0.559 12.282 36859 Z= 0.297 Chirality : 0.042 0.312 4088 Planarity : 0.004 0.035 3818 Dihedral : 25.475 172.114 6056 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.15 % Allowed : 21.08 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.18), residues: 2396 helix: 2.22 (0.16), residues: 1178 sheet: -0.79 (0.85), residues: 36 loop : -0.02 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 456 TYR 0.008 0.001 TYR C 39 PHE 0.009 0.001 PHE O 86 TRP 0.007 0.001 TRP O 89 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (26304) covalent geometry : angle 0.55189 / 0.30 (36805) SS BOND : bond 0.00893 / 0.43 ( 6) SS BOND : angle 0.99736 / 0.56 ( 12) hydrogen bonds : bond 0.04851 / 3.33 ( 1184) hydrogen bonds : angle 4.05422 / 2.88 ( 3129) Misc. bond : bond 0.17543 / 9.10 ( 3) link_ALPHA1-3 : bond 0.00944 / 0.50 ( 1) link_ALPHA1-3 : angle 2.43727 / 1.38 ( 3) link_ALPHA1-6 : bond 0.00815 / 0.41 ( 2) link_ALPHA1-6 : angle 1.82637 / 0.92 ( 6) link_BETA1-4 : bond 0.00545 / 0.27 ( 4) link_BETA1-4 : angle 2.18108 / 1.44 ( 12) link_BETA1-6 : bond 0.00210 / 0.10 ( 2) link_BETA1-6 : angle 1.54130 / 0.87 ( 6) link_NAG-ASN : bond 0.00619 / 0.33 ( 5) link_NAG-ASN : angle 3.58256 / 1.99 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 285 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8023 (mtm-85) cc_final: 0.7816 (mmm-85) REVERT: B 27 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8796 (mp10) REVERT: C 73 ASN cc_start: 0.8262 (t0) cc_final: 0.8009 (t0) REVERT: F 35 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7961 (mtp85) REVERT: G 15 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8524 (pttp) REVERT: K 27 ARG cc_start: 0.8791 (mmm-85) cc_final: 0.8586 (mmt90) REVERT: K 41 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7715 (m-80) REVERT: L 263 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7682 (tt0) REVERT: N 447 THR cc_start: 0.8617 (p) cc_final: 0.8406 (t) REVERT: O 38 GLU cc_start: 0.8517 (tt0) cc_final: 0.8099 (tt0) REVERT: O 48 THR cc_start: 0.9152 (m) cc_final: 0.8816 (p) REVERT: O 52 LYS cc_start: 0.8756 (mtmp) cc_final: 0.8471 (mttp) REVERT: O 67 GLU cc_start: 0.8276 (mp0) cc_final: 0.7835 (mp0) REVERT: O 70 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8309 (ttt90) REVERT: O 80 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8217 (mp10) REVERT: P 169 SER cc_start: 0.8668 (m) cc_final: 0.8315 (p) REVERT: P 214 ASP cc_start: 0.7841 (t0) cc_final: 0.7593 (t0) outliers start: 66 outliers final: 46 residues processed: 337 average time/residue: 0.2195 time to fit residues: 108.7695 Evaluate side-chains 327 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 41 PHE Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 221 CYS Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 543 ILE Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 262 THR Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 540 ASN Chi-restraints excluded: chain N residue 545 THR Chi-restraints excluded: chain N residue 554 SER Chi-restraints excluded: chain N residue 566 THR Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 238 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 377 ILE Chi-restraints excluded: chain P residue 545 THR Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 193 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 213 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 243 optimal weight: 0.8980 chunk 208 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 71 optimal weight: 40.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN K 26 ASN K 91 GLN K 95 HIS ** L 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 326 ASN L 550 ASN M 54 ASN O 54 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.097294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.073778 restraints weight = 51821.705| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.77 r_work: 0.2902 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.242 26327 Z= 0.171 Angle : 0.576 10.903 36859 Z= 0.300 Chirality : 0.042 0.334 4088 Planarity : 0.004 0.033 3818 Dihedral : 25.448 172.347 6020 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.87 % Allowed : 19.69 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % 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: 1.52 (0.18), residues: 2396 helix: 2.21 (0.16), residues: 1180 sheet: -0.88 (0.84), residues: 36 loop : -0.14 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 8 TYR 0.011 0.001 TYR C 39 PHE 0.010 0.001 PHE O 86 TRP 0.008 0.001 TRP M 89 HIS 0.004 0.001 HIS L 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (26304) covalent geometry : angle 0.56992 / 0.30 (36805) SS BOND : bond 0.00377 / 0.22 ( 6) SS BOND : angle 0.77865 / 0.42 ( 12) hydrogen bonds : bond 0.04930 / 3.39 ( 1184) hydrogen bonds : angle 3.87819 / 2.75 ( 3129) Misc. bond : bond 0.15520 / 8.08 ( 3) link_ALPHA1-3 : bond 0.01014 / 0.53 ( 1) link_ALPHA1-3 : angle 2.68385 / 1.50 ( 3) link_ALPHA1-6 : bond 0.00688 / 0.34 ( 2) link_ALPHA1-6 : angle 2.36510 / 1.16 ( 6) link_BETA1-4 : bond 0.00451 / 0.22 ( 4) link_BETA1-4 : angle 2.42414 / 1.56 ( 12) link_BETA1-6 : bond 0.00272 / 0.14 ( 2) link_BETA1-6 : angle 1.56911 / 0.92 ( 6) link_NAG-ASN : bond 0.00440 / 0.26 ( 5) link_NAG-ASN : angle 2.90722 / 1.62 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 280 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7786 (mmm-85) REVERT: B 24 ASP cc_start: 0.7526 (p0) cc_final: 0.7311 (p0) REVERT: C 73 ASN cc_start: 0.8313 (t0) cc_final: 0.8025 (t0) REVERT: D 110 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: E 131 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.7853 (mtp85) REVERT: F 35 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8018 (mtp85) REVERT: G 15 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8512 (pttp) REVERT: K 41 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: K 79 ASP cc_start: 0.8289 (t0) cc_final: 0.8062 (t0) REVERT: L 263 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7702 (tt0) REVERT: L 312 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8110 (m) REVERT: N 447 THR cc_start: 0.8637 (p) cc_final: 0.8428 (t) REVERT: O 38 GLU cc_start: 0.8544 (tt0) cc_final: 0.8111 (tt0) REVERT: O 48 THR cc_start: 0.9166 (m) cc_final: 0.8802 (p) REVERT: O 52 LYS cc_start: 0.8780 (mtmp) cc_final: 0.8488 (mttp) REVERT: O 67 GLU cc_start: 0.8292 (mp0) cc_final: 0.7837 (mp0) REVERT: O 70 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8317 (ttt90) REVERT: O 80 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8240 (mp10) REVERT: P 169 SER cc_start: 0.8723 (m) cc_final: 0.8358 (p) REVERT: P 214 ASP cc_start: 0.7867 (t0) cc_final: 0.7606 (t0) outliers start: 81 outliers final: 61 residues processed: 345 average time/residue: 0.2170 time to fit residues: 109.8602 Evaluate side-chains 340 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 274 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 41 PHE Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 543 ILE Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 566 THR Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 150 CYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 262 THR Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 540 ASN Chi-restraints excluded: chain N residue 545 THR Chi-restraints excluded: chain N residue 554 SER Chi-restraints excluded: chain N residue 566 THR Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 238 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 377 ILE Chi-restraints excluded: chain P residue 545 THR Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 117 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN F 25 ASN K 95 HIS L 201 GLN ** L 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 550 ASN M 54 ASN O 54 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.098089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.074592 restraints weight = 51517.400| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.81 r_work: 0.2914 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.239 26327 Z= 0.130 Angle : 0.543 10.135 36859 Z= 0.287 Chirality : 0.041 0.329 4088 Planarity : 0.004 0.039 3818 Dihedral : 25.374 172.567 6019 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.20 % Allowed : 20.46 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % 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: 1.58 (0.18), residues: 2396 helix: 2.28 (0.16), residues: 1180 sheet: -0.79 (0.85), residues: 36 loop : -0.14 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 456 TYR 0.008 0.001 TYR H 37 PHE 0.009 0.001 PHE O 86 TRP 0.008 0.001 TRP M 89 HIS 0.005 0.001 HIS K 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (26304) covalent geometry : angle 0.53740 / 0.29 (36805) SS BOND : bond 0.00310 / 0.19 ( 6) SS BOND : angle 0.82287 / 0.47 ( 12) hydrogen bonds : bond 0.04410 / 3.05 ( 1184) hydrogen bonds : angle 3.74921 / 2.66 ( 3129) Misc. bond : bond 0.16036 / 8.30 ( 3) link_ALPHA1-3 : bond 0.01225 / 0.64 ( 1) link_ALPHA1-3 : angle 2.76744 / 1.53 ( 3) link_ALPHA1-6 : bond 0.00625 / 0.32 ( 2) link_ALPHA1-6 : angle 2.32057 / 1.13 ( 6) link_BETA1-4 : bond 0.00482 / 0.24 ( 4) link_BETA1-4 : angle 2.22508 / 1.44 ( 12) link_BETA1-6 : bond 0.00191 / 0.09 ( 2) link_BETA1-6 : angle 1.55764 / 0.88 ( 6) link_NAG-ASN : bond 0.00478 / 0.25 ( 5) link_NAG-ASN : angle 2.76715 / 1.52 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 281 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7565 (p0) cc_final: 0.7305 (p0) REVERT: C 73 ASN cc_start: 0.8275 (t0) cc_final: 0.7966 (t0) REVERT: D 110 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: E 131 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.7838 (mtp85) REVERT: F 35 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8031 (mtp85) REVERT: G 15 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8492 (pttp) REVERT: L 263 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7716 (tt0) REVERT: L 353 MET cc_start: 0.6062 (ttp) cc_final: 0.5553 (ttp) REVERT: O 38 GLU cc_start: 0.8538 (tt0) cc_final: 0.8101 (tt0) REVERT: O 48 THR cc_start: 0.9153 (m) cc_final: 0.8792 (p) REVERT: O 52 LYS cc_start: 0.8776 (mtmp) cc_final: 0.8476 (mttp) REVERT: O 67 GLU cc_start: 0.8304 (mp0) cc_final: 0.7852 (mp0) REVERT: O 70 ARG cc_start: 0.8602 (ttp80) cc_final: 0.8313 (ttt90) REVERT: O 80 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8215 (mp10) REVERT: P 169 SER cc_start: 0.8671 (m) cc_final: 0.8304 (p) REVERT: P 214 ASP cc_start: 0.7867 (t0) cc_final: 0.7626 (t0) outliers start: 67 outliers final: 53 residues processed: 330 average time/residue: 0.2197 time to fit residues: 106.0689 Evaluate side-chains 326 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 270 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 543 ILE Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 150 CYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 262 THR Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 540 ASN Chi-restraints excluded: chain N residue 545 THR Chi-restraints excluded: chain N residue 566 THR Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain P residue 137 ILE Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 238 THR Chi-restraints excluded: chain P residue 377 ILE Chi-restraints excluded: chain P residue 545 THR Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 258 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 158 optimal weight: 0.9990 chunk 167 optimal weight: 0.4980 chunk 1 optimal weight: 8.9990 chunk 230 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN K 26 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN O 54 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.098469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.075077 restraints weight = 51672.798| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.79 r_work: 0.2935 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.243 26327 Z= 0.122 Angle : 0.534 10.804 36859 Z= 0.282 Chirality : 0.040 0.329 4088 Planarity : 0.004 0.038 3818 Dihedral : 25.307 172.673 6017 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.11 % Allowed : 20.60 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % 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: 1.66 (0.18), residues: 2396 helix: 2.37 (0.16), residues: 1180 sheet: -0.77 (0.85), residues: 36 loop : -0.13 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 456 TYR 0.014 0.001 TYR K 45 PHE 0.009 0.001 PHE O 86 TRP 0.007 0.001 TRP M 89 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (26304) covalent geometry : angle 0.52857 / 0.28 (36805) SS BOND : bond 0.00362 / 0.21 ( 6) SS BOND : angle 1.09874 / 0.60 ( 12) hydrogen bonds : bond 0.04195 / 2.90 ( 1184) hydrogen bonds : angle 3.65905 / 2.59 ( 3129) Misc. bond : bond 0.16227 / 8.40 ( 3) link_ALPHA1-3 : bond 0.01643 / 0.86 ( 1) link_ALPHA1-3 : angle 2.41472 / 1.24 ( 3) link_ALPHA1-6 : bond 0.00821 / 0.42 ( 2) link_ALPHA1-6 : angle 2.38411 / 1.17 ( 6) link_BETA1-4 : bond 0.00437 / 0.22 ( 4) link_BETA1-4 : angle 2.20016 / 1.45 ( 12) link_BETA1-6 : bond 0.00129 / 0.06 ( 2) link_BETA1-6 : angle 1.52819 / 0.86 ( 6) link_NAG-ASN : bond 0.00469 / 0.24 ( 5) link_NAG-ASN : angle 2.67403 / 1.45 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 285 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7529 (p0) cc_final: 0.7222 (p0) REVERT: C 73 ASN cc_start: 0.8261 (t0) cc_final: 0.7940 (t0) REVERT: D 110 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: F 35 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8046 (mtp85) REVERT: G 15 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8488 (pttp) REVERT: L 263 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7688 (tt0) REVERT: L 353 MET cc_start: 0.6045 (ttp) cc_final: 0.5524 (ttp) REVERT: M 27 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8611 (mmt90) REVERT: O 38 GLU cc_start: 0.8537 (tt0) cc_final: 0.8075 (tt0) REVERT: O 48 THR cc_start: 0.9148 (m) cc_final: 0.8793 (p) REVERT: O 52 LYS cc_start: 0.8757 (mtmp) cc_final: 0.8449 (mttp) REVERT: O 66 ASN cc_start: 0.8463 (m-40) cc_final: 0.8248 (m-40) REVERT: O 67 GLU cc_start: 0.8305 (mp0) cc_final: 0.7863 (mp0) REVERT: O 70 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8305 (ttt90) REVERT: O 80 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8230 (mp10) REVERT: P 169 SER cc_start: 0.8677 (m) cc_final: 0.8315 (p) REVERT: P 214 ASP cc_start: 0.7834 (t0) cc_final: 0.7602 (t0) outliers start: 65 outliers final: 54 residues processed: 337 average time/residue: 0.2169 time to fit residues: 107.3149 Evaluate side-chains 333 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 276 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 543 ILE Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 150 CYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 262 THR Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 540 ASN Chi-restraints excluded: chain N residue 545 THR Chi-restraints excluded: chain N residue 564 CYS Chi-restraints excluded: chain N residue 566 THR Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 238 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 377 ILE Chi-restraints excluded: chain P residue 545 THR Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 115 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 242 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 227 optimal weight: 0.2980 chunk 183 optimal weight: 0.0870 chunk 117 optimal weight: 0.9990 chunk 228 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN F 25 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.103004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.079272 restraints weight = 54295.491| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.84 r_work: 0.2993 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.226 26327 Z= 0.108 Angle : 0.519 9.169 36859 Z= 0.276 Chirality : 0.040 0.326 4088 Planarity : 0.004 0.041 3818 Dihedral : 25.240 172.779 6017 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.53 % Allowed : 21.41 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % 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: 1.75 (0.18), residues: 2396 helix: 2.44 (0.16), residues: 1180 sheet: -0.69 (0.86), residues: 36 loop : -0.08 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG P 456 TYR 0.008 0.001 TYR H 37 PHE 0.009 0.001 PHE O 86 TRP 0.009 0.001 TRP M 89 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 (26304) covalent geometry : angle 0.51301 / 0.27 (36805) SS BOND : bond 0.00783 / 0.41 ( 6) SS BOND : angle 0.79856 / 0.47 ( 12) hydrogen bonds : bond 0.03884 / 2.70 ( 1184) hydrogen bonds : angle 3.55583 / 2.52 ( 3129) Misc. bond : bond 0.15456 / 7.98 ( 3) link_ALPHA1-3 : bond 0.01510 / 0.79 ( 1) link_ALPHA1-3 : angle 2.53443 / 1.30 ( 3) link_ALPHA1-6 : bond 0.01127 / 0.58 ( 2) link_ALPHA1-6 : angle 2.41531 / 1.21 ( 6) link_BETA1-4 : bond 0.00443 / 0.22 ( 4) link_BETA1-4 : angle 2.08504 / 1.39 ( 12) link_BETA1-6 : bond 0.00058 / 0.03 ( 2) link_BETA1-6 : angle 1.52703 / 0.85 ( 6) link_NAG-ASN : bond 0.00514 / 0.26 ( 5) link_NAG-ASN : angle 2.62012 / 1.41 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 289 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7624 (p0) cc_final: 0.7305 (p0) REVERT: C 73 ASN cc_start: 0.8293 (t0) cc_final: 0.7976 (t0) REVERT: D 110 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: E 131 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.7829 (mtp85) REVERT: G 15 LYS cc_start: 0.8881 (mtmt) cc_final: 0.8484 (pttp) REVERT: L 263 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7714 (tt0) REVERT: M 27 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8617 (mmt90) REVERT: O 38 GLU cc_start: 0.8658 (tt0) cc_final: 0.8205 (tt0) REVERT: O 48 THR cc_start: 0.9161 (m) cc_final: 0.8813 (p) REVERT: O 52 LYS cc_start: 0.8800 (mtmp) cc_final: 0.8487 (mttp) REVERT: O 67 GLU cc_start: 0.8497 (mp0) cc_final: 0.8144 (mp0) REVERT: O 70 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8381 (ttt90) REVERT: O 80 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8369 (mp10) REVERT: P 169 SER cc_start: 0.8693 (m) cc_final: 0.8344 (p) REVERT: P 214 ASP cc_start: 0.7920 (t0) cc_final: 0.7686 (t0) outliers start: 53 outliers final: 42 residues processed: 327 average time/residue: 0.2181 time to fit residues: 104.0773 Evaluate side-chains 325 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 280 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 543 ILE Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 150 CYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 554 SER Chi-restraints excluded: chain N residue 564 CYS Chi-restraints excluded: chain N residue 566 THR Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 238 THR Chi-restraints excluded: chain P residue 545 THR Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 212 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 230 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 257 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN K 26 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.096995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.073483 restraints weight = 51304.388| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.80 r_work: 0.2887 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.200 26327 Z= 0.181 Angle : 0.577 12.474 36859 Z= 0.298 Chirality : 0.042 0.346 4088 Planarity : 0.004 0.044 3818 Dihedral : 25.328 172.647 6012 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.49 % Allowed : 20.55 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.18), residues: 2396 helix: 2.31 (0.16), residues: 1178 sheet: -0.84 (0.85), residues: 36 loop : -0.18 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG P 456 TYR 0.012 0.001 TYR K 45 PHE 0.011 0.001 PHE H 62 TRP 0.018 0.001 TRP L 514 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (26304) covalent geometry : angle 0.57129 / 0.30 (36805) SS BOND : bond 0.00356 / 0.22 ( 6) SS BOND : angle 1.20099 / 0.72 ( 12) hydrogen bonds : bond 0.04733 / 3.27 ( 1184) hydrogen bonds : angle 3.70625 / 2.63 ( 3129) Misc. bond : bond 0.13494 / 6.99 ( 3) link_ALPHA1-3 : bond 0.01210 / 0.64 ( 1) link_ALPHA1-3 : angle 1.72814 / 0.87 ( 3) link_ALPHA1-6 : bond 0.00897 / 0.46 ( 2) link_ALPHA1-6 : angle 2.66663 / 1.33 ( 6) link_BETA1-4 : bond 0.00392 / 0.19 ( 4) link_BETA1-4 : angle 2.45964 / 1.59 ( 12) link_BETA1-6 : bond 0.00369 / 0.19 ( 2) link_BETA1-6 : angle 1.65417 / 0.96 ( 6) link_NAG-ASN : bond 0.00439 / 0.25 ( 5) link_NAG-ASN : angle 2.73471 / 1.48 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 270 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7930 (mmm-85) cc_final: 0.7103 (mpp-170) REVERT: B 24 ASP cc_start: 0.7585 (p0) cc_final: 0.7275 (p0) REVERT: C 73 ASN cc_start: 0.8273 (t0) cc_final: 0.7920 (t0) REVERT: D 110 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: E 131 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.7836 (mtp85) REVERT: F 35 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8097 (mtp85) REVERT: G 15 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8435 (pttp) REVERT: L 263 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7694 (tt0) REVERT: O 38 GLU cc_start: 0.8569 (tt0) cc_final: 0.8114 (tt0) REVERT: O 48 THR cc_start: 0.9147 (m) cc_final: 0.8748 (p) REVERT: O 52 LYS cc_start: 0.8790 (mtmp) cc_final: 0.8472 (mttp) REVERT: O 67 GLU cc_start: 0.8342 (mp0) cc_final: 0.7894 (mp0) REVERT: O 80 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8237 (mp10) REVERT: P 169 SER cc_start: 0.8747 (m) cc_final: 0.8367 (p) REVERT: P 214 ASP cc_start: 0.7812 (t0) cc_final: 0.7590 (t0) outliers start: 73 outliers final: 60 residues processed: 326 average time/residue: 0.2082 time to fit residues: 100.0516 Evaluate side-chains 328 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 265 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 137 ILE Chi-restraints excluded: chain N residue 150 CYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 262 THR Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 454 VAL Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 564 CYS Chi-restraints excluded: chain N residue 566 THR Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain P residue 137 ILE Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 238 THR Chi-restraints excluded: chain P residue 377 ILE Chi-restraints excluded: chain P residue 545 THR Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 12 optimal weight: 0.7980 chunk 179 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 chunk 217 optimal weight: 0.2980 chunk 136 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 72 optimal weight: 30.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS C 104 GLN D 81 ASN F 25 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN O 54 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.102315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.078589 restraints weight = 54067.697| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.83 r_work: 0.2990 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.198 26327 Z= 0.111 Angle : 0.532 8.327 36859 Z= 0.281 Chirality : 0.040 0.330 4088 Planarity : 0.004 0.045 3818 Dihedral : 25.248 172.368 6010 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.39 % Allowed : 21.70 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % 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: 1.71 (0.18), residues: 2396 helix: 2.42 (0.16), residues: 1177 sheet: -0.69 (0.86), residues: 36 loop : -0.12 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG P 456 TYR 0.008 0.001 TYR H 37 PHE 0.010 0.001 PHE O 86 TRP 0.015 0.001 TRP L 514 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (26304) covalent geometry : angle 0.52682 / 0.28 (36805) SS BOND : bond 0.00356 / 0.20 ( 6) SS BOND : angle 0.88934 / 0.53 ( 12) hydrogen bonds : bond 0.04012 / 2.78 ( 1184) hydrogen bonds : angle 3.56109 / 2.53 ( 3129) Misc. bond : bond 0.14559 / 7.47 ( 3) link_ALPHA1-3 : bond 0.01191 / 0.63 ( 1) link_ALPHA1-3 : angle 2.25363 / 1.15 ( 3) link_ALPHA1-6 : bond 0.01187 / 0.61 ( 2) link_ALPHA1-6 : angle 2.39108 / 1.20 ( 6) link_BETA1-4 : bond 0.00481 / 0.24 ( 4) link_BETA1-4 : angle 2.09746 / 1.40 ( 12) link_BETA1-6 : bond 0.00087 / 0.04 ( 2) link_BETA1-6 : angle 1.60089 / 0.88 ( 6) link_NAG-ASN : bond 0.00518 / 0.26 ( 5) link_NAG-ASN : angle 2.63401 / 1.42 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 275 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8007 (mmm-85) cc_final: 0.7089 (mpp-170) REVERT: B 24 ASP cc_start: 0.7675 (p0) cc_final: 0.7345 (p0) REVERT: C 73 ASN cc_start: 0.8300 (t0) cc_final: 0.7957 (t0) REVERT: D 110 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: E 131 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.7858 (mtp85) REVERT: F 35 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8212 (mtp85) REVERT: G 15 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8416 (pttp) REVERT: L 263 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7673 (tt0) REVERT: L 353 MET cc_start: 0.6055 (ttp) cc_final: 0.5524 (ttp) REVERT: O 38 GLU cc_start: 0.8650 (tt0) cc_final: 0.8199 (tt0) REVERT: O 48 THR cc_start: 0.9161 (m) cc_final: 0.8802 (p) REVERT: O 52 LYS cc_start: 0.8827 (mtmp) cc_final: 0.8506 (mttp) REVERT: O 67 GLU cc_start: 0.8511 (mp0) cc_final: 0.8057 (mp0) REVERT: O 70 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8150 (ttt90) REVERT: O 80 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8379 (mp10) REVERT: P 169 SER cc_start: 0.8698 (m) cc_final: 0.8345 (p) REVERT: P 214 ASP cc_start: 0.7897 (t0) cc_final: 0.7683 (t0) outliers start: 50 outliers final: 45 residues processed: 313 average time/residue: 0.2014 time to fit residues: 92.8745 Evaluate side-chains 320 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 150 CYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 554 SER Chi-restraints excluded: chain N residue 564 CYS Chi-restraints excluded: chain N residue 566 THR Chi-restraints excluded: chain P residue 137 ILE Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 238 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 545 THR Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 151 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 200 optimal weight: 2.9990 chunk 213 optimal weight: 0.0020 chunk 161 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 81 ASN F 25 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 550 ASN M 54 ASN O 54 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.098021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.074637 restraints weight = 51503.999| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.80 r_work: 0.2925 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.186 26327 Z= 0.139 Angle : 0.547 9.591 36859 Z= 0.285 Chirality : 0.041 0.337 4088 Planarity : 0.004 0.045 3818 Dihedral : 25.242 172.350 6010 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.53 % Allowed : 21.51 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % 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: 1.77 (0.18), residues: 2396 helix: 2.52 (0.16), residues: 1159 sheet: -0.73 (0.85), residues: 36 loop : -0.10 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG P 456 TYR 0.008 0.001 TYR H 37 PHE 0.009 0.001 PHE O 86 TRP 0.017 0.001 TRP L 514 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (26304) covalent geometry : angle 0.54148 / 0.28 (36805) SS BOND : bond 0.00368 / 0.21 ( 6) SS BOND : angle 0.94452 / 0.56 ( 12) hydrogen bonds : bond 0.04219 / 2.92 ( 1184) hydrogen bonds : angle 3.58861 / 2.55 ( 3129) Misc. bond : bond 0.13042 / 6.73 ( 3) link_ALPHA1-3 : bond 0.01187 / 0.62 ( 1) link_ALPHA1-3 : angle 1.98400 / 1.01 ( 3) link_ALPHA1-6 : bond 0.01143 / 0.59 ( 2) link_ALPHA1-6 : angle 2.49647 / 1.26 ( 6) link_BETA1-4 : bond 0.00430 / 0.21 ( 4) link_BETA1-4 : angle 2.22780 / 1.45 ( 12) link_BETA1-6 : bond 0.00222 / 0.11 ( 2) link_BETA1-6 : angle 1.59392 / 0.90 ( 6) link_NAG-ASN : bond 0.00444 / 0.23 ( 5) link_NAG-ASN : angle 2.65531 / 1.43 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 273 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7986 (mmm-85) cc_final: 0.7085 (mpp-170) REVERT: B 24 ASP cc_start: 0.7733 (p0) cc_final: 0.7404 (p0) REVERT: C 15 LYS cc_start: 0.9141 (ptpp) cc_final: 0.8816 (mttt) REVERT: C 73 ASN cc_start: 0.8292 (t0) cc_final: 0.7930 (t0) REVERT: D 110 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: E 131 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.7897 (mtp85) REVERT: F 35 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8235 (mtp85) REVERT: G 15 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8388 (pttp) REVERT: L 263 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7677 (tt0) REVERT: O 38 GLU cc_start: 0.8700 (tt0) cc_final: 0.8248 (tt0) REVERT: O 48 THR cc_start: 0.9147 (m) cc_final: 0.8772 (p) REVERT: O 52 LYS cc_start: 0.8826 (mtmp) cc_final: 0.8505 (mttp) REVERT: O 67 GLU cc_start: 0.8587 (mp0) cc_final: 0.8203 (mp0) REVERT: O 80 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8391 (mp10) REVERT: P 169 SER cc_start: 0.8768 (m) cc_final: 0.8391 (p) REVERT: P 214 ASP cc_start: 0.7989 (t0) cc_final: 0.7761 (t0) outliers start: 53 outliers final: 47 residues processed: 313 average time/residue: 0.2197 time to fit residues: 100.6769 Evaluate side-chains 320 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 270 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 150 CYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 554 SER Chi-restraints excluded: chain N residue 564 CYS Chi-restraints excluded: chain N residue 566 THR Chi-restraints excluded: chain P residue 137 ILE Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 238 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 545 THR Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 68.698 > 50: distance: 33 - 34: 4.379 distance: 34 - 35: 13.745 distance: 34 - 37: 3.682 distance: 35 - 36: 29.084 distance: 35 - 42: 19.578 distance: 38 - 39: 4.852 distance: 39 - 40: 3.159 distance: 39 - 41: 4.683 distance: 42 - 43: 18.092 distance: 43 - 44: 17.895 distance: 43 - 46: 12.076 distance: 44 - 45: 21.604 distance: 44 - 51: 36.368 distance: 46 - 47: 8.971 distance: 47 - 48: 6.905 distance: 48 - 49: 3.638 distance: 48 - 50: 5.321 distance: 51 - 52: 30.562 distance: 51 - 57: 9.015 distance: 52 - 53: 32.507 distance: 52 - 55: 13.225 distance: 53 - 54: 21.035 distance: 53 - 58: 40.034 distance: 55 - 56: 8.619 distance: 56 - 57: 25.075 distance: 58 - 59: 6.486 distance: 58 - 64: 15.093 distance: 59 - 60: 20.699 distance: 59 - 62: 28.086 distance: 60 - 61: 47.087 distance: 60 - 65: 18.131 distance: 62 - 63: 16.316 distance: 63 - 64: 16.438 distance: 65 - 66: 12.792 distance: 66 - 67: 39.211 distance: 66 - 69: 17.090 distance: 67 - 68: 25.485 distance: 67 - 71: 41.101 distance: 69 - 70: 34.733 distance: 71 - 72: 19.616 distance: 72 - 73: 38.093 distance: 72 - 75: 21.480 distance: 73 - 82: 45.645 distance: 75 - 76: 14.028 distance: 76 - 77: 11.489 distance: 76 - 78: 17.135 distance: 77 - 79: 12.507 distance: 78 - 80: 3.709 distance: 79 - 81: 9.620 distance: 80 - 81: 15.098 distance: 82 - 83: 4.560 distance: 83 - 84: 30.109 distance: 83 - 86: 17.005 distance: 84 - 85: 17.399 distance: 84 - 89: 8.824 distance: 86 - 87: 9.832 distance: 87 - 88: 11.868 distance: 89 - 90: 4.642 distance: 90 - 91: 16.817 distance: 90 - 93: 6.095 distance: 91 - 92: 19.227 distance: 91 - 97: 25.294 distance: 93 - 94: 4.873 distance: 94 - 95: 6.166 distance: 94 - 96: 16.036 distance: 98 - 99: 5.822 distance: 98 - 101: 11.123 distance: 99 - 100: 8.699 distance: 99 - 106: 22.886 distance: 101 - 102: 10.441 distance: 102 - 103: 12.752 distance: 103 - 104: 4.402