Starting phenix.real_space_refine on Thu Sep 18 23:34:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9geq_51301/09_2025/9geq_51301.cif Found real_map, /net/cci-nas-00/data/ceres_data/9geq_51301/09_2025/9geq_51301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9geq_51301/09_2025/9geq_51301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9geq_51301/09_2025/9geq_51301.map" model { file = "/net/cci-nas-00/data/ceres_data/9geq_51301/09_2025/9geq_51301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9geq_51301/09_2025/9geq_51301.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.264 sd= 1.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 2 7.16 5 P 266 5.49 5 S 76 5.16 5 Cl 2 4.86 5 C 12310 2.51 5 N 3844 2.21 5 O 4386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20888 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2743 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "J" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2710 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 837 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 10, 'TRANS': 93} Chain: "N" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3732 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 429} Chain: "K" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 837 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 10, 'TRANS': 93} Chain: "L" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3732 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 429} Chain: "O" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {' CL': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 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: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {' CL': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 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: 4.77, per 1000 atoms: 0.23 Number of scatterers: 20888 At special positions: 0 Unit cell: (123.76, 125.8, 150.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 2 26.01 Ca 2 19.99 Cl 2 17.00 S 76 16.00 P 266 15.00 O 4386 8.00 N 3844 7.00 C 12310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS M 1 " - pdb=" SG CYS M 14 " distance=2.03 Simple disulfide: pdb=" SG CYS N 115 " - pdb=" SG CYS N 125 " distance=2.03 Simple disulfide: pdb=" SG CYS N 119 " - pdb=" SG CYS N 143 " distance=2.03 Simple disulfide: pdb=" SG CYS N 153 " - pdb=" SG CYS L 153 " distance=2.03 Simple disulfide: pdb=" SG CYS N 221 " - pdb=" SG CYS N 232 " distance=2.03 Simple disulfide: pdb=" SG CYS N 440 " - pdb=" SG CYS N 497 " distance=2.03 Simple disulfide: pdb=" SG CYS N 538 " - pdb=" SG CYS N 564 " distance=2.03 Simple disulfide: pdb=" SG CYS K 1 " - pdb=" SG CYS K 14 " distance=2.03 Simple disulfide: pdb=" SG CYS L 115 " - pdb=" SG CYS L 125 " distance=2.03 Simple disulfide: pdb=" SG CYS L 119 " - pdb=" SG CYS L 143 " distance=2.03 Simple disulfide: pdb=" SG CYS L 221 " - pdb=" SG CYS L 232 " distance=2.03 Simple disulfide: pdb=" SG CYS L 440 " - pdb=" SG CYS L 497 " distance=2.03 Simple disulfide: pdb=" SG CYS L 538 " - pdb=" SG CYS L 564 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=9, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 5 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " BETA1-6 " NAG O 1 " - " FUC O 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 6 " NAG-ASN " NAG L 601 " - " ASN L 189 " " NAG L 602 " - " ASN L 225 " " NAG N 601 " - " ASN N 189 " " NAG N 602 " - " ASN N 225 " " NAG O 1 " - " ASN N 317 " " NAG P 1 " - " ASN L 317 " Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 658.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3564 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 21 sheets defined 56.2% alpha, 3.4% beta 128 base pairs and 219 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.833A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.509A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.707A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.667A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.036A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.515A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.796A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.509A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.639A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.816A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 68 Processing helix chain 'M' and resid 72 through 76 Processing helix chain 'M' and resid 84 through 98 Processing helix chain 'N' and resid 173 through 178 removed outlier: 3.533A pdb=" N TYR N 177 " --> pdb=" O ALA N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 187 Processing helix chain 'N' and resid 219 through 225 removed outlier: 3.935A pdb=" N LEU N 223 " --> pdb=" O ASP N 219 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR N 224 " --> pdb=" O PRO N 220 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASN N 225 " --> pdb=" O CYS N 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 219 through 225' Processing helix chain 'N' and resid 243 through 268 Processing helix chain 'N' and resid 272 through 295 Processing helix chain 'N' and resid 295 through 302 removed outlier: 4.038A pdb=" N LEU N 299 " --> pdb=" O ASP N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 302 through 310 Processing helix chain 'N' and resid 325 through 332 removed outlier: 3.758A pdb=" N THR N 329 " --> pdb=" O ALA N 325 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN N 330 " --> pdb=" O ASN N 326 " (cutoff:3.500A) Processing helix chain 'N' and resid 333 through 338 Processing helix chain 'N' and resid 362 through 364 No H-bonds generated for 'chain 'N' and resid 362 through 364' Processing helix chain 'N' and resid 367 through 374 removed outlier: 3.890A pdb=" N VAL N 371 " --> pdb=" O ALA N 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 377 through 386 Processing helix chain 'N' and resid 400 through 405 Processing helix chain 'N' and resid 416 through 428 Processing helix chain 'N' and resid 432 through 440 Processing helix chain 'N' and resid 447 through 456 Processing helix chain 'N' and resid 457 through 469 Processing helix chain 'N' and resid 470 through 474 Processing helix chain 'N' and resid 475 through 483 Processing helix chain 'N' and resid 492 through 509 Processing helix chain 'N' and resid 521 through 529 Processing helix chain 'N' and resid 532 through 541 Processing helix chain 'N' and resid 565 through 567 No H-bonds generated for 'chain 'N' and resid 565 through 567' Processing helix chain 'N' and resid 572 through 576 Processing helix chain 'K' and resid 60 through 68 Processing helix chain 'K' and resid 72 through 76 Processing helix chain 'K' and resid 84 through 98 Processing helix chain 'L' and resid 173 through 178 Processing helix chain 'L' and resid 180 through 187 Processing helix chain 'L' and resid 220 through 225 removed outlier: 3.909A pdb=" N THR L 224 " --> pdb=" O PRO L 220 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN L 225 " --> pdb=" O CYS L 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 220 through 225' Processing helix chain 'L' and resid 243 through 268 Processing helix chain 'L' and resid 272 through 296 Processing helix chain 'L' and resid 296 through 302 Processing helix chain 'L' and resid 302 through 310 Processing helix chain 'L' and resid 327 through 332 Processing helix chain 'L' and resid 333 through 338 Processing helix chain 'L' and resid 362 through 364 No H-bonds generated for 'chain 'L' and resid 362 through 364' Processing helix chain 'L' and resid 368 through 374 Processing helix chain 'L' and resid 377 through 386 Processing helix chain 'L' and resid 399 through 405 Processing helix chain 'L' and resid 416 through 428 Processing helix chain 'L' and resid 432 through 440 Processing helix chain 'L' and resid 447 through 456 Processing helix chain 'L' and resid 457 through 469 Processing helix chain 'L' and resid 470 through 474 Processing helix chain 'L' and resid 475 through 483 Processing helix chain 'L' and resid 492 through 509 Processing helix chain 'L' and resid 521 through 529 Processing helix chain 'L' and resid 532 through 541 Processing helix chain 'L' and resid 565 through 567 No H-bonds generated for 'chain 'L' and resid 565 through 567' Processing helix chain 'L' and resid 571 through 576 removed outlier: 4.355A pdb=" N SER L 574 " --> pdb=" O ASN L 571 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.826A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.536A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.254A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.750A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.902A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.145A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 27 through 28 Processing sheet with id=AB3, first strand: chain 'M' and resid 52 through 53 Processing sheet with id=AB4, first strand: chain 'M' and resid 78 through 83 removed outlier: 4.238A pdb=" N ALA N 389 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 128 through 129 Processing sheet with id=AB6, first strand: chain 'N' and resid 342 through 344 Processing sheet with id=AB7, first strand: chain 'N' and resid 545 through 547 Processing sheet with id=AB8, first strand: chain 'K' and resid 27 through 28 Processing sheet with id=AB9, first strand: chain 'K' and resid 78 through 83 removed outlier: 3.979A pdb=" N ALA L 389 " --> pdb=" O ASP K 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 128 through 129 Processing sheet with id=AC2, first strand: chain 'L' and resid 342 through 344 Processing sheet with id=AC3, first strand: chain 'L' and resid 545 through 547 728 hydrogen bonds defined for protein. 2097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 326 hydrogen bonds 652 hydrogen bond angles 0 basepair planarities 128 basepair parallelities 219 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 8430 1.39 - 1.56: 12773 1.56 - 1.74: 530 1.74 - 1.91: 122 1.91 - 2.08: 8 Bond restraints: 21863 Sorted by residual: bond pdb=" CG GLN L 193 " pdb=" CD GLN L 193 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.27e+00 bond pdb=" C5 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.413 1.385 0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" CG ASN L 192 " pdb=" ND2 ASN L 192 " ideal model delta sigma weight residual 1.328 1.357 -0.029 2.10e-02 2.27e+03 1.93e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" C5 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.413 1.386 0.027 2.00e-02 2.50e+03 1.82e+00 ... (remaining 21858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 30640 3.04 - 6.08: 116 6.08 - 9.12: 8 9.12 - 12.16: 1 12.16 - 15.20: 1 Bond angle restraints: 30766 Sorted by residual: angle pdb=" CA GLU L 242 " pdb=" CB GLU L 242 " pdb=" CG GLU L 242 " ideal model delta sigma weight residual 114.10 122.62 -8.52 2.00e+00 2.50e-01 1.81e+01 angle pdb=" CB GLU L 242 " pdb=" CG GLU L 242 " pdb=" CD GLU L 242 " ideal model delta sigma weight residual 112.60 106.02 6.58 1.70e+00 3.46e-01 1.50e+01 angle pdb=" C GLU N 242 " pdb=" CA GLU N 242 " pdb=" CB GLU N 242 " ideal model delta sigma weight residual 110.92 105.51 5.41 1.59e+00 3.96e-01 1.16e+01 angle pdb=" C MET L 243 " pdb=" CA MET L 243 " pdb=" CB MET L 243 " ideal model delta sigma weight residual 110.17 116.18 -6.01 1.97e+00 2.58e-01 9.32e+00 angle pdb=" C3B HEM K 202 " pdb=" CAB HEM K 202 " pdb=" CBB HEM K 202 " ideal model delta sigma weight residual 120.00 128.90 -8.90 3.00e+00 1.11e-01 8.81e+00 ... (remaining 30761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.15: 11121 34.15 - 68.29: 1604 68.29 - 102.44: 43 102.44 - 136.58: 1 136.58 - 170.73: 2 Dihedral angle restraints: 12771 sinusoidal: 7262 harmonic: 5509 Sorted by residual: dihedral pdb=" CA GLU L 242 " pdb=" C GLU L 242 " pdb=" N MET L 243 " pdb=" CA MET L 243 " ideal model delta harmonic sigma weight residual -180.00 -139.34 -40.66 0 5.00e+00 4.00e-02 6.61e+01 dihedral pdb=" CB CYS N 153 " pdb=" SG CYS N 153 " pdb=" SG CYS L 153 " pdb=" CB CYS L 153 " ideal model delta sinusoidal sigma weight residual -86.00 -146.37 60.37 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CA GLU N 242 " pdb=" C GLU N 242 " pdb=" N MET N 243 " pdb=" CA MET N 243 " ideal model delta harmonic sigma weight residual -180.00 -146.53 -33.47 0 5.00e+00 4.00e-02 4.48e+01 ... (remaining 12768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3007 0.052 - 0.104: 386 0.104 - 0.155: 52 0.155 - 0.207: 3 0.207 - 0.259: 4 Chirality restraints: 3452 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN N 317 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1 NAG N 601 " pdb=" ND2 ASN N 189 " pdb=" C2 NAG N 601 " pdb=" O5 NAG N 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.05 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3449 not shown) Planarity restraints: 3030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN N 317 " -0.039 2.00e-02 2.50e+03 3.70e-02 1.71e+01 pdb=" CG ASN N 317 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN N 317 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN N 317 " 0.047 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN L 317 " 0.038 2.00e-02 2.50e+03 3.50e-02 1.53e+01 pdb=" CG ASN L 317 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN L 317 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN L 317 " -0.045 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN N 225 " 0.023 2.00e-02 2.50e+03 2.10e-02 5.52e+00 pdb=" CG ASN N 225 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN N 225 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN N 225 " -0.015 2.00e-02 2.50e+03 pdb=" C1 NAG N 602 " 0.019 2.00e-02 2.50e+03 ... (remaining 3027 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 516 2.68 - 3.24: 18520 3.24 - 3.79: 36762 3.79 - 4.35: 48836 4.35 - 4.90: 75067 Nonbonded interactions: 179701 Sorted by model distance: nonbonded pdb=" O ILE N 537 " pdb=" OG1 THR N 541 " model vdw 2.127 3.040 nonbonded pdb=" O ILE L 537 " pdb=" OG1 THR L 541 " model vdw 2.153 3.040 nonbonded pdb=" OE1 GLU L 242 " pdb=" CMB HEM K 202 " model vdw 2.197 2.768 nonbonded pdb=" OH TYR N 433 " pdb=" OE2 GLU N 483 " model vdw 2.219 3.040 nonbonded pdb=" OE2 GLU M 38 " pdb=" OG1 THR M 48 " model vdw 2.230 3.040 ... (remaining 179696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.910 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.003 0.199 21901 Z= 0.130 Angle : 0.598 15.202 30840 Z= 0.310 Chirality : 0.037 0.259 3452 Planarity : 0.004 0.063 3024 Dihedral : 23.891 170.729 9168 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.53 % Allowed : 23.30 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.20), residues: 1873 helix: 2.15 (0.17), residues: 976 sheet: None (None), residues: 0 loop : 0.37 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 559 TYR 0.011 0.001 TYR H 37 PHE 0.012 0.001 PHE K 86 TRP 0.007 0.001 TRP L 436 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00279 (21863) covalent geometry : angle 0.56793 (30766) SS BOND : bond 0.00210 ( 13) SS BOND : angle 0.73490 ( 26) hydrogen bonds : bond 0.11648 ( 1054) hydrogen bonds : angle 5.00112 ( 2749) Misc. bond : bond 0.07488 ( 9) link_ALPHA1-3 : bond 0.01284 ( 2) link_ALPHA1-3 : angle 1.45367 ( 6) link_ALPHA1-6 : bond 0.00844 ( 2) link_ALPHA1-6 : angle 1.38505 ( 6) link_BETA1-4 : bond 0.00646 ( 4) link_BETA1-4 : angle 1.84157 ( 12) link_BETA1-6 : bond 0.00205 ( 2) link_BETA1-6 : angle 2.20598 ( 6) link_NAG-ASN : bond 0.01088 ( 6) link_NAG-ASN : angle 7.50349 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 243 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8659 (mptt) cc_final: 0.8115 (mmtm) REVERT: C 64 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: C 92 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8026 (mm-30) REVERT: F 92 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8132 (ttp80) REVERT: H 68 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: H 88 SER cc_start: 0.9013 (t) cc_final: 0.8796 (m) REVERT: N 539 ASP cc_start: 0.7964 (m-30) cc_final: 0.7613 (m-30) REVERT: N 572 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8857 (mt) REVERT: L 267 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8004 (mp) REVERT: L 446 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7432 (tm-30) outliers start: 25 outliers final: 16 residues processed: 257 average time/residue: 0.2129 time to fit residues: 74.6572 Evaluate side-chains 259 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 243 MET Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 572 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 267 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 446 GLU Chi-restraints excluded: chain L residue 497 CYS Chi-restraints excluded: chain L residue 541 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS E 68 GLN F 25 ASN G 104 GLN L 206 ASN ** L 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.111981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.084230 restraints weight = 31788.346| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.63 r_work: 0.2903 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.219 21901 Z= 0.233 Angle : 0.626 15.796 30840 Z= 0.328 Chirality : 0.040 0.249 3452 Planarity : 0.005 0.041 3024 Dihedral : 25.974 173.600 5407 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.31 % Allowed : 20.48 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.20), residues: 1873 helix: 2.00 (0.17), residues: 988 sheet: None (None), residues: 0 loop : 0.19 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 559 TYR 0.014 0.002 TYR D 34 PHE 0.017 0.002 PHE K 86 TRP 0.008 0.001 TRP M 89 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00563 (21863) covalent geometry : angle 0.60849 (30766) SS BOND : bond 0.00463 ( 13) SS BOND : angle 1.06822 ( 26) hydrogen bonds : bond 0.04667 ( 1054) hydrogen bonds : angle 3.97746 ( 2749) Misc. bond : bond 0.07786 ( 9) link_ALPHA1-3 : bond 0.00889 ( 2) link_ALPHA1-3 : angle 1.69189 ( 6) link_ALPHA1-6 : bond 0.00375 ( 2) link_ALPHA1-6 : angle 1.70613 ( 6) link_BETA1-4 : bond 0.00248 ( 4) link_BETA1-4 : angle 2.74766 ( 12) link_BETA1-6 : bond 0.00212 ( 2) link_BETA1-6 : angle 1.47558 ( 6) link_NAG-ASN : bond 0.00774 ( 6) link_NAG-ASN : angle 5.49444 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 233 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7670 (mtt) REVERT: G 15 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8448 (mttm) REVERT: N 219 ASP cc_start: 0.7707 (t70) cc_final: 0.7477 (t70) REVERT: N 237 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7899 (t0) REVERT: N 256 GLU cc_start: 0.8410 (tp30) cc_final: 0.8166 (tp30) REVERT: N 411 MET cc_start: 0.8128 (mtt) cc_final: 0.7758 (mtt) REVERT: N 539 ASP cc_start: 0.7947 (m-30) cc_final: 0.7561 (m-30) REVERT: L 254 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8701 (tp) REVERT: L 446 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7704 (tm-30) outliers start: 54 outliers final: 33 residues processed: 270 average time/residue: 0.1920 time to fit residues: 71.9775 Evaluate side-chains 269 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 237 ASP Chi-restraints excluded: chain N residue 243 MET Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 465 MET Chi-restraints excluded: chain N residue 497 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 446 GLU Chi-restraints excluded: chain L residue 497 CYS Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 566 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 48 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN G 104 GLN H 106 HIS L 206 ASN ** L 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 526 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.085914 restraints weight = 31580.870| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.64 r_work: 0.2931 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.182 21901 Z= 0.135 Angle : 0.568 15.630 30840 Z= 0.301 Chirality : 0.037 0.245 3452 Planarity : 0.004 0.057 3024 Dihedral : 26.002 176.367 5379 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.49 % Allowed : 19.56 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.20), residues: 1873 helix: 2.20 (0.17), residues: 988 sheet: None (None), residues: 0 loop : 0.26 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 349 TYR 0.011 0.001 TYR D 34 PHE 0.013 0.001 PHE K 86 TRP 0.009 0.001 TRP N 436 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00300 (21863) covalent geometry : angle 0.55437 (30766) SS BOND : bond 0.00258 ( 13) SS BOND : angle 0.67880 ( 26) hydrogen bonds : bond 0.03858 ( 1054) hydrogen bonds : angle 3.76133 ( 2749) Misc. bond : bond 0.06992 ( 9) link_ALPHA1-3 : bond 0.01175 ( 2) link_ALPHA1-3 : angle 1.65423 ( 6) link_ALPHA1-6 : bond 0.00637 ( 2) link_ALPHA1-6 : angle 1.52656 ( 6) link_BETA1-4 : bond 0.00226 ( 4) link_BETA1-4 : angle 2.00589 ( 12) link_BETA1-6 : bond 0.00052 ( 2) link_BETA1-6 : angle 1.51698 ( 6) link_NAG-ASN : bond 0.01535 ( 6) link_NAG-ASN : angle 4.67627 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 238 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8359 (mtt) cc_final: 0.8058 (mtt) REVERT: F 25 ASN cc_start: 0.8822 (m-40) cc_final: 0.8604 (m-40) REVERT: G 15 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8356 (mttm) REVERT: N 219 ASP cc_start: 0.7673 (t70) cc_final: 0.7292 (t70) REVERT: N 237 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7868 (t0) REVERT: N 265 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8132 (tptp) REVERT: N 411 MET cc_start: 0.8092 (mtt) cc_final: 0.7713 (mtt) REVERT: N 539 ASP cc_start: 0.7894 (m-30) cc_final: 0.7522 (m-30) REVERT: K 52 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8777 (mttp) REVERT: L 254 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8671 (tp) REVERT: L 446 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: L 490 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8087 (mmt180) outliers start: 57 outliers final: 34 residues processed: 279 average time/residue: 0.2045 time to fit residues: 79.1584 Evaluate side-chains 272 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 237 ASP Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 265 LYS Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 465 MET Chi-restraints excluded: chain N residue 497 CYS Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 577 GLU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 330 ASN Chi-restraints excluded: chain L residue 446 GLU Chi-restraints excluded: chain L residue 490 ARG Chi-restraints excluded: chain L residue 497 CYS Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 574 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 149 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN L 206 ASN ** L 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.113976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.085714 restraints weight = 31580.590| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.67 r_work: 0.2949 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.225 21901 Z= 0.141 Angle : 0.561 15.161 30840 Z= 0.296 Chirality : 0.037 0.228 3452 Planarity : 0.004 0.041 3024 Dihedral : 26.019 176.178 5376 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.25 % Allowed : 19.25 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.20), residues: 1873 helix: 2.32 (0.17), residues: 988 sheet: None (None), residues: 0 loop : 0.30 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 30 TYR 0.010 0.001 TYR D 34 PHE 0.012 0.001 PHE N 342 TRP 0.008 0.001 TRP N 436 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00325 (21863) covalent geometry : angle 0.54663 (30766) SS BOND : bond 0.00280 ( 13) SS BOND : angle 0.84400 ( 26) hydrogen bonds : bond 0.03732 ( 1054) hydrogen bonds : angle 3.59868 ( 2749) Misc. bond : bond 0.07974 ( 9) link_ALPHA1-3 : bond 0.01114 ( 2) link_ALPHA1-3 : angle 1.68836 ( 6) link_ALPHA1-6 : bond 0.00638 ( 2) link_ALPHA1-6 : angle 1.53509 ( 6) link_BETA1-4 : bond 0.00368 ( 4) link_BETA1-4 : angle 2.02000 ( 12) link_BETA1-6 : bond 0.00065 ( 2) link_BETA1-6 : angle 1.59439 ( 6) link_NAG-ASN : bond 0.00836 ( 6) link_NAG-ASN : angle 4.67568 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 238 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8315 (mtt) cc_final: 0.8045 (mtt) REVERT: F 92 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8189 (ttp80) REVERT: F 93 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8153 (mp10) REVERT: G 15 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8346 (mttm) REVERT: G 113 SER cc_start: 0.8073 (OUTLIER) cc_final: 0.7706 (p) REVERT: H 83 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8068 (mtt-85) REVERT: N 121 GLN cc_start: 0.8031 (tt0) cc_final: 0.7799 (tt0) REVERT: N 219 ASP cc_start: 0.7632 (t70) cc_final: 0.7339 (t70) REVERT: N 265 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8121 (tptp) REVERT: N 358 ARG cc_start: 0.8447 (mtp-110) cc_final: 0.7459 (ttp80) REVERT: N 539 ASP cc_start: 0.7821 (m-30) cc_final: 0.7425 (m-30) REVERT: N 562 VAL cc_start: 0.8085 (m) cc_final: 0.7884 (p) REVERT: K 52 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8783 (mttp) REVERT: L 254 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8671 (tp) REVERT: L 267 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8157 (mp) REVERT: L 446 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.8007 (tp30) REVERT: L 490 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8110 (mmt180) outliers start: 53 outliers final: 36 residues processed: 275 average time/residue: 0.2079 time to fit residues: 78.4105 Evaluate side-chains 277 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 265 LYS Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 465 MET Chi-restraints excluded: chain N residue 497 CYS Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 577 GLU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 267 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 330 ASN Chi-restraints excluded: chain L residue 446 GLU Chi-restraints excluded: chain L residue 490 ARG Chi-restraints excluded: chain L residue 497 CYS Chi-restraints excluded: chain L residue 566 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 121 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 191 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN L 206 ASN ** L 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.113655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.085437 restraints weight = 31620.171| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.66 r_work: 0.2945 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 21901 Z= 0.151 Angle : 0.551 14.437 30840 Z= 0.294 Chirality : 0.037 0.232 3452 Planarity : 0.004 0.041 3024 Dihedral : 26.081 175.160 5376 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.74 % Allowed : 18.95 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.20), residues: 1873 helix: 2.33 (0.17), residues: 987 sheet: None (None), residues: 0 loop : 0.28 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 559 TYR 0.011 0.001 TYR D 34 PHE 0.012 0.001 PHE K 86 TRP 0.007 0.001 TRP L 436 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00351 (21863) covalent geometry : angle 0.53772 (30766) SS BOND : bond 0.00263 ( 13) SS BOND : angle 0.77740 ( 26) hydrogen bonds : bond 0.03763 ( 1054) hydrogen bonds : angle 3.56117 ( 2749) Misc. bond : bond 0.06529 ( 9) link_ALPHA1-3 : bond 0.01215 ( 2) link_ALPHA1-3 : angle 1.66267 ( 6) link_ALPHA1-6 : bond 0.00621 ( 2) link_ALPHA1-6 : angle 1.53383 ( 6) link_BETA1-4 : bond 0.00292 ( 4) link_BETA1-4 : angle 2.08486 ( 12) link_BETA1-6 : bond 0.00094 ( 2) link_BETA1-6 : angle 1.59685 ( 6) link_NAG-ASN : bond 0.00612 ( 6) link_NAG-ASN : angle 4.34781 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 236 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8333 (mtt) cc_final: 0.8079 (mtt) REVERT: F 92 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8039 (ttp80) REVERT: F 93 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8183 (mp10) REVERT: G 15 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8346 (mttm) REVERT: G 113 SER cc_start: 0.8031 (OUTLIER) cc_final: 0.7664 (p) REVERT: H 83 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8045 (mtt-85) REVERT: N 121 GLN cc_start: 0.8019 (tt0) cc_final: 0.7806 (tt0) REVERT: N 219 ASP cc_start: 0.7623 (t70) cc_final: 0.7328 (t70) REVERT: N 237 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7843 (t0) REVERT: N 265 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8109 (tptp) REVERT: N 400 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8274 (t0) REVERT: N 539 ASP cc_start: 0.7837 (m-30) cc_final: 0.7440 (m-30) REVERT: K 52 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8802 (mttp) REVERT: L 254 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8655 (tp) REVERT: L 267 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8162 (mp) REVERT: L 490 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8104 (mmt90) outliers start: 61 outliers final: 41 residues processed: 276 average time/residue: 0.2015 time to fit residues: 77.4303 Evaluate side-chains 284 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 237 ASP Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 265 LYS Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 447 THR Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 465 MET Chi-restraints excluded: chain N residue 497 CYS Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 577 GLU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 267 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 330 ASN Chi-restraints excluded: chain L residue 490 ARG Chi-restraints excluded: chain L residue 497 CYS Chi-restraints excluded: chain L residue 566 THR Chi-restraints excluded: chain L residue 574 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN G 104 GLN L 206 ASN ** L 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 526 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.111481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.083458 restraints weight = 31610.143| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.62 r_work: 0.2902 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.208 21901 Z= 0.216 Angle : 0.595 12.841 30840 Z= 0.315 Chirality : 0.039 0.244 3452 Planarity : 0.004 0.044 3024 Dihedral : 26.290 176.989 5373 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.05 % Allowed : 18.64 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.20), residues: 1873 helix: 2.11 (0.17), residues: 988 sheet: None (None), residues: 0 loop : 0.20 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 559 TYR 0.014 0.001 TYR D 34 PHE 0.014 0.001 PHE K 86 TRP 0.008 0.001 TRP M 89 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00522 (21863) covalent geometry : angle 0.58193 (30766) SS BOND : bond 0.00346 ( 13) SS BOND : angle 0.91010 ( 26) hydrogen bonds : bond 0.04425 ( 1054) hydrogen bonds : angle 3.70356 ( 2749) Misc. bond : bond 0.07369 ( 9) link_ALPHA1-3 : bond 0.00926 ( 2) link_ALPHA1-3 : angle 1.72443 ( 6) link_ALPHA1-6 : bond 0.00333 ( 2) link_ALPHA1-6 : angle 1.71076 ( 6) link_BETA1-4 : bond 0.00242 ( 4) link_BETA1-4 : angle 2.27306 ( 12) link_BETA1-6 : bond 0.00283 ( 2) link_BETA1-6 : angle 1.64853 ( 6) link_NAG-ASN : bond 0.00621 ( 6) link_NAG-ASN : angle 4.42934 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 229 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8427 (mtt) cc_final: 0.8206 (mtt) REVERT: E 120 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7904 (mtt) REVERT: F 92 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8006 (ttp80) REVERT: F 93 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8184 (mp10) REVERT: G 15 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8393 (mttm) REVERT: G 92 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8027 (mt-10) REVERT: G 113 SER cc_start: 0.8008 (OUTLIER) cc_final: 0.7666 (p) REVERT: H 83 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8089 (mtt-85) REVERT: N 139 ASN cc_start: 0.7735 (t0) cc_final: 0.7410 (t0) REVERT: N 219 ASP cc_start: 0.7755 (t70) cc_final: 0.7505 (t70) REVERT: N 237 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7926 (t0) REVERT: N 265 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8162 (tptp) REVERT: N 330 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8712 (m-40) REVERT: N 400 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8323 (t0) REVERT: N 539 ASP cc_start: 0.7874 (m-30) cc_final: 0.7464 (m-30) REVERT: K 52 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8813 (mttp) REVERT: L 254 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8651 (tp) REVERT: L 490 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8064 (mmt90) outliers start: 66 outliers final: 44 residues processed: 273 average time/residue: 0.1981 time to fit residues: 74.6950 Evaluate side-chains 285 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 228 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 237 ASP Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 265 LYS Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 447 THR Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 465 MET Chi-restraints excluded: chain N residue 497 CYS Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 330 ASN Chi-restraints excluded: chain L residue 490 ARG Chi-restraints excluded: chain L residue 497 CYS Chi-restraints excluded: chain L residue 546 VAL Chi-restraints excluded: chain L residue 566 THR Chi-restraints excluded: chain L residue 574 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 105 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 159 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN G 104 GLN L 206 ASN ** L 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.085488 restraints weight = 31489.528| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.62 r_work: 0.2942 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.192 21901 Z= 0.136 Angle : 0.556 12.999 30840 Z= 0.297 Chirality : 0.036 0.222 3452 Planarity : 0.004 0.044 3024 Dihedral : 26.212 173.752 5373 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.49 % Allowed : 19.07 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.20), residues: 1873 helix: 2.30 (0.17), residues: 988 sheet: None (None), residues: 0 loop : 0.25 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 559 TYR 0.011 0.001 TYR H 37 PHE 0.011 0.001 PHE K 86 TRP 0.009 0.001 TRP M 47 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00309 (21863) covalent geometry : angle 0.54415 (30766) SS BOND : bond 0.00243 ( 13) SS BOND : angle 0.70575 ( 26) hydrogen bonds : bond 0.03693 ( 1054) hydrogen bonds : angle 3.53531 ( 2749) Misc. bond : bond 0.06873 ( 9) link_ALPHA1-3 : bond 0.01084 ( 2) link_ALPHA1-3 : angle 1.71436 ( 6) link_ALPHA1-6 : bond 0.00606 ( 2) link_ALPHA1-6 : angle 1.55453 ( 6) link_BETA1-4 : bond 0.00350 ( 4) link_BETA1-4 : angle 2.00560 ( 12) link_BETA1-6 : bond 0.00153 ( 2) link_BETA1-6 : angle 1.56761 ( 6) link_NAG-ASN : bond 0.01187 ( 6) link_NAG-ASN : angle 4.18243 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8138 (ttp80) REVERT: G 15 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8361 (mttm) REVERT: G 92 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: G 113 SER cc_start: 0.7980 (OUTLIER) cc_final: 0.7662 (p) REVERT: H 83 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8068 (mtt-85) REVERT: N 139 ASN cc_start: 0.7785 (t0) cc_final: 0.7434 (t0) REVERT: N 219 ASP cc_start: 0.7684 (t70) cc_final: 0.7432 (t70) REVERT: N 265 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8117 (tptp) REVERT: N 363 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8202 (mmp80) REVERT: N 400 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8289 (t0) REVERT: N 539 ASP cc_start: 0.7827 (m-30) cc_final: 0.7395 (m-30) REVERT: K 52 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8807 (mttp) REVERT: L 254 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8643 (tp) outliers start: 57 outliers final: 39 residues processed: 278 average time/residue: 0.2027 time to fit residues: 77.7975 Evaluate side-chains 283 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 234 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 265 LYS Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 363 ARG Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 417 LEU Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 456 ARG Chi-restraints excluded: chain N residue 465 MET Chi-restraints excluded: chain N residue 485 LEU Chi-restraints excluded: chain N residue 497 CYS Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 577 GLU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 330 ASN Chi-restraints excluded: chain L residue 497 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 167 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN G 104 GLN L 206 ASN ** L 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.113441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085331 restraints weight = 31358.080| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.65 r_work: 0.2944 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.186 21901 Z= 0.148 Angle : 0.574 14.837 30840 Z= 0.299 Chirality : 0.037 0.226 3452 Planarity : 0.004 0.043 3024 Dihedral : 26.183 173.239 5373 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.13 % Allowed : 19.56 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.20), residues: 1873 helix: 2.31 (0.17), residues: 988 sheet: None (None), residues: 0 loop : 0.28 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 42 TYR 0.010 0.001 TYR D 34 PHE 0.011 0.001 PHE M 86 TRP 0.008 0.001 TRP L 436 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00344 (21863) covalent geometry : angle 0.56265 (30766) SS BOND : bond 0.00277 ( 13) SS BOND : angle 0.73326 ( 26) hydrogen bonds : bond 0.03731 ( 1054) hydrogen bonds : angle 3.51865 ( 2749) Misc. bond : bond 0.06643 ( 9) link_ALPHA1-3 : bond 0.01144 ( 2) link_ALPHA1-3 : angle 1.74168 ( 6) link_ALPHA1-6 : bond 0.00595 ( 2) link_ALPHA1-6 : angle 1.54609 ( 6) link_BETA1-4 : bond 0.00304 ( 4) link_BETA1-4 : angle 2.06076 ( 12) link_BETA1-6 : bond 0.00181 ( 2) link_BETA1-6 : angle 1.61354 ( 6) link_NAG-ASN : bond 0.00947 ( 6) link_NAG-ASN : angle 4.21540 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8081 (ttp80) REVERT: G 15 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8368 (mttm) REVERT: G 92 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: G 113 SER cc_start: 0.7976 (OUTLIER) cc_final: 0.7660 (p) REVERT: H 83 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8033 (mtt-85) REVERT: N 139 ASN cc_start: 0.7822 (t0) cc_final: 0.7459 (t0) REVERT: N 219 ASP cc_start: 0.7657 (t70) cc_final: 0.7403 (t70) REVERT: N 265 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8097 (tptp) REVERT: N 363 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8213 (mmp80) REVERT: N 400 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8296 (t0) REVERT: N 539 ASP cc_start: 0.7823 (m-30) cc_final: 0.7406 (m-30) REVERT: K 52 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8807 (mttp) REVERT: L 254 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8644 (tp) outliers start: 51 outliers final: 41 residues processed: 271 average time/residue: 0.2103 time to fit residues: 78.2651 Evaluate side-chains 282 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 265 LYS Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 363 ARG Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 417 LEU Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 456 ARG Chi-restraints excluded: chain N residue 465 MET Chi-restraints excluded: chain N residue 485 LEU Chi-restraints excluded: chain N residue 497 CYS Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 577 GLU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 330 ASN Chi-restraints excluded: chain L residue 497 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 171 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN L 206 ASN ** L 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.112483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.084416 restraints weight = 31458.554| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.69 r_work: 0.2926 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 21901 Z= 0.176 Angle : 0.588 14.594 30840 Z= 0.308 Chirality : 0.038 0.233 3452 Planarity : 0.004 0.044 3024 Dihedral : 26.230 172.511 5373 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.31 % Allowed : 19.25 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.20), residues: 1873 helix: 2.31 (0.17), residues: 975 sheet: None (None), residues: 0 loop : 0.24 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 42 TYR 0.012 0.001 TYR D 34 PHE 0.012 0.001 PHE K 86 TRP 0.007 0.001 TRP K 89 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00417 (21863) covalent geometry : angle 0.57607 (30766) SS BOND : bond 0.00306 ( 13) SS BOND : angle 0.79981 ( 26) hydrogen bonds : bond 0.04011 ( 1054) hydrogen bonds : angle 3.57808 ( 2749) Misc. bond : bond 0.05840 ( 9) link_ALPHA1-3 : bond 0.01059 ( 2) link_ALPHA1-3 : angle 1.74882 ( 6) link_ALPHA1-6 : bond 0.00477 ( 2) link_ALPHA1-6 : angle 1.61331 ( 6) link_BETA1-4 : bond 0.00268 ( 4) link_BETA1-4 : angle 2.15685 ( 12) link_BETA1-6 : bond 0.00219 ( 2) link_BETA1-6 : angle 1.62387 ( 6) link_NAG-ASN : bond 0.00836 ( 6) link_NAG-ASN : angle 4.39860 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 231 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 40 LYS cc_start: 0.8838 (mttt) cc_final: 0.8469 (mttm) REVERT: F 92 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8049 (ttp80) REVERT: G 15 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8376 (mttm) REVERT: G 92 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: G 113 SER cc_start: 0.7948 (OUTLIER) cc_final: 0.7636 (p) REVERT: H 83 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8094 (mtt-85) REVERT: N 139 ASN cc_start: 0.7884 (t0) cc_final: 0.7516 (t0) REVERT: N 219 ASP cc_start: 0.7711 (t70) cc_final: 0.7456 (t70) REVERT: N 237 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7902 (t0) REVERT: N 265 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8068 (tptp) REVERT: N 363 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8239 (mmp80) REVERT: N 400 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8320 (t0) REVERT: N 539 ASP cc_start: 0.7829 (m-30) cc_final: 0.7407 (m-30) REVERT: K 52 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8810 (mttp) REVERT: L 254 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8648 (tp) outliers start: 54 outliers final: 42 residues processed: 270 average time/residue: 0.2198 time to fit residues: 81.4167 Evaluate side-chains 283 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 237 ASP Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 265 LYS Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 363 ARG Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 417 LEU Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 465 MET Chi-restraints excluded: chain N residue 485 LEU Chi-restraints excluded: chain N residue 497 CYS Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain L residue 142 ASP Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 330 ASN Chi-restraints excluded: chain L residue 497 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 76 optimal weight: 6.9990 chunk 176 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN L 206 ASN ** L 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.112117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.084005 restraints weight = 31645.319| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.69 r_work: 0.2918 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 21901 Z= 0.186 Angle : 0.592 13.967 30840 Z= 0.310 Chirality : 0.038 0.236 3452 Planarity : 0.004 0.046 3024 Dihedral : 26.246 172.401 5373 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.43 % Allowed : 19.01 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 1.92 (0.20), residues: 1873 helix: 2.28 (0.17), residues: 973 sheet: None (None), residues: 0 loop : 0.21 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG N 349 TYR 0.010 0.001 TYR D 34 PHE 0.013 0.001 PHE K 86 TRP 0.007 0.001 TRP K 89 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00445 (21863) covalent geometry : angle 0.57976 (30766) SS BOND : bond 0.00496 ( 13) SS BOND : angle 0.81063 ( 26) hydrogen bonds : bond 0.04078 ( 1054) hydrogen bonds : angle 3.58877 ( 2749) Misc. bond : bond 0.05647 ( 9) link_ALPHA1-3 : bond 0.01029 ( 2) link_ALPHA1-3 : angle 1.76745 ( 6) link_ALPHA1-6 : bond 0.00470 ( 2) link_ALPHA1-6 : angle 1.66957 ( 6) link_BETA1-4 : bond 0.00242 ( 4) link_BETA1-4 : angle 2.18005 ( 12) link_BETA1-6 : bond 0.00288 ( 2) link_BETA1-6 : angle 1.60923 ( 6) link_NAG-ASN : bond 0.00819 ( 6) link_NAG-ASN : angle 4.46118 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 229 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 40 LYS cc_start: 0.8867 (mttt) cc_final: 0.8500 (mttm) REVERT: E 120 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7862 (mtt) REVERT: F 92 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8045 (ttp80) REVERT: G 15 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8378 (mttm) REVERT: G 92 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: G 113 SER cc_start: 0.7910 (OUTLIER) cc_final: 0.7597 (p) REVERT: H 83 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8095 (mtt-85) REVERT: N 139 ASN cc_start: 0.7933 (t0) cc_final: 0.7594 (t0) REVERT: N 219 ASP cc_start: 0.7716 (t70) cc_final: 0.7464 (t70) REVERT: N 237 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7915 (t0) REVERT: N 265 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8132 (tptp) REVERT: N 363 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8186 (mmp80) REVERT: N 400 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8338 (t0) REVERT: N 464 LEU cc_start: 0.8626 (mm) cc_final: 0.8379 (mt) REVERT: N 539 ASP cc_start: 0.7849 (m-30) cc_final: 0.7418 (m-30) REVERT: K 52 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8808 (mttp) REVERT: L 254 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8637 (tp) outliers start: 56 outliers final: 44 residues processed: 269 average time/residue: 0.2181 time to fit residues: 80.8758 Evaluate side-chains 286 residues out of total 1631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 230 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 87 MET Chi-restraints excluded: chain N residue 113 VAL Chi-restraints excluded: chain N residue 159 THR Chi-restraints excluded: chain N residue 206 ASN Chi-restraints excluded: chain N residue 237 ASP Chi-restraints excluded: chain N residue 260 LEU Chi-restraints excluded: chain N residue 265 LYS Chi-restraints excluded: chain N residue 346 LEU Chi-restraints excluded: chain N residue 363 ARG Chi-restraints excluded: chain N residue 387 THR Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 410 VAL Chi-restraints excluded: chain N residue 417 LEU Chi-restraints excluded: chain N residue 448 VAL Chi-restraints excluded: chain N residue 465 MET Chi-restraints excluded: chain N residue 485 LEU Chi-restraints excluded: chain N residue 497 CYS Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 577 GLU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain L residue 142 ASP Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 330 ASN Chi-restraints excluded: chain L residue 497 CYS Chi-restraints excluded: chain L residue 566 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 44 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 187 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 164 optimal weight: 0.4980 chunk 16 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 172 optimal weight: 0.0670 chunk 204 optimal weight: 0.0870 chunk 59 optimal weight: 0.6980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN G 104 GLN L 206 ASN ** L 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.086101 restraints weight = 31362.434| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.68 r_work: 0.2960 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.134 21901 Z= 0.123 Angle : 0.558 12.426 30840 Z= 0.296 Chirality : 0.036 0.210 3452 Planarity : 0.004 0.066 3024 Dihedral : 26.191 173.057 5373 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.58 % Allowed : 19.80 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: 2.16 (0.20), residues: 1873 helix: 2.49 (0.17), residues: 974 sheet: None (None), residues: 0 loop : 0.31 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 349 TYR 0.013 0.001 TYR H 37 PHE 0.012 0.001 PHE M 86 TRP 0.011 0.001 TRP L 436 HIS 0.002 0.000 HIS N 257 Details of bonding type rmsd covalent geometry : bond 0.00272 (21863) covalent geometry : angle 0.54652 (30766) SS BOND : bond 0.00221 ( 13) SS BOND : angle 0.53543 ( 26) hydrogen bonds : bond 0.03556 ( 1054) hydrogen bonds : angle 3.45277 ( 2749) Misc. bond : bond 0.05396 ( 9) link_ALPHA1-3 : bond 0.01208 ( 2) link_ALPHA1-3 : angle 1.80329 ( 6) link_ALPHA1-6 : bond 0.00759 ( 2) link_ALPHA1-6 : angle 1.47990 ( 6) link_BETA1-4 : bond 0.00328 ( 4) link_BETA1-4 : angle 1.96139 ( 12) link_BETA1-6 : bond 0.00059 ( 2) link_BETA1-6 : angle 1.61334 ( 6) link_NAG-ASN : bond 0.00885 ( 6) link_NAG-ASN : angle 4.26166 ( 18) =============================================================================== Job complete usr+sys time: 5516.03 seconds wall clock time: 94 minutes 41.74 seconds (5681.74 seconds total)