Starting phenix.real_space_refine on Fri Sep 19 11:26:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ihf_52870/09_2025/9ihf_52870.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ihf_52870/09_2025/9ihf_52870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ihf_52870/09_2025/9ihf_52870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ihf_52870/09_2025/9ihf_52870.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ihf_52870/09_2025/9ihf_52870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ihf_52870/09_2025/9ihf_52870.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.342 sd= 1.208 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 3 7.16 5 P 266 5.49 5 S 99 5.16 5 C 15061 2.51 5 N 4632 2.21 5 O 5152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s 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: 25213 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2743 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "J" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2710 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 806 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "L" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3670 Classifications: {'peptide': 457} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 420} Chain: "M" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 806 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "N" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3670 Classifications: {'peptide': 457} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 420} Chain: "O" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 806 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "P" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3670 Classifications: {'peptide': 457} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 420} Chain: "Q" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Unusual residues: {'HEM': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'HEM': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'HEM': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.71, per 1000 atoms: 0.23 Number of scatterers: 25213 At special positions: 0 Unit cell: (138.04, 123.08, 169.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 3 26.01 S 99 16.00 P 266 15.00 O 5152 8.00 N 4632 7.00 C 15061 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 221 " - pdb=" SG CYS L 232 " distance=2.03 Simple disulfide: pdb=" SG CYS L 440 " - pdb=" SG CYS L 497 " distance=2.03 Simple disulfide: pdb=" SG CYS N 221 " - pdb=" SG CYS N 232 " distance=2.03 Simple disulfide: pdb=" SG CYS N 440 " - pdb=" SG CYS N 497 " distance=2.03 Simple disulfide: pdb=" SG CYS N 538 " - pdb=" SG CYS N 564 " distance=2.03 Simple disulfide: pdb=" SG CYS P 221 " - pdb=" SG CYS P 232 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " ALPHA1-6 " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 4 " BETA1-4 " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " BETA1-6 " NAG Q 1 " - " FUC Q 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG R 1 " - " FUC R 5 " NAG-ASN " NAG L 603 " - " ASN L 189 " " NAG L 604 " - " ASN L 317 " " NAG N 603 " - " ASN N 189 " " NAG Q 1 " - " ASN N 317 " " NAG R 1 " - " ASN P 317 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4550 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 23 sheets defined 53.6% alpha, 2.7% beta 123 base pairs and 225 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.083A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.506A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.622A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.546A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.609A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.564A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.875A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.935A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.568A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.504A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 35 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.743A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 68 Processing helix chain 'K' and resid 72 through 76 Processing helix chain 'K' and resid 84 through 98 Processing helix chain 'L' and resid 173 through 178 Processing helix chain 'L' and resid 180 through 187 Processing helix chain 'L' and resid 221 through 225 removed outlier: 3.852A pdb=" N THR L 224 " --> pdb=" O CYS L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 268 Processing helix chain 'L' and resid 272 through 302 removed outlier: 5.539A pdb=" N LEU L 297 " --> pdb=" O TYR L 293 " (cutoff:3.500A) Proline residue: L 298 - end of helix Processing helix chain 'L' and resid 302 through 310 Processing helix chain 'L' and resid 327 through 332 Processing helix chain 'L' and resid 333 through 338 Processing helix chain 'L' and resid 362 through 364 No H-bonds generated for 'chain 'L' and resid 362 through 364' Processing helix chain 'L' and resid 368 through 373 Processing helix chain 'L' and resid 377 through 386 Processing helix chain 'L' and resid 400 through 405 Processing helix chain 'L' and resid 416 through 428 Processing helix chain 'L' and resid 432 through 440 Processing helix chain 'L' and resid 447 through 456 Processing helix chain 'L' and resid 458 through 469 Processing helix chain 'L' and resid 470 through 474 Processing helix chain 'L' and resid 475 through 483 Processing helix chain 'L' and resid 492 through 509 Processing helix chain 'L' and resid 521 through 529 Processing helix chain 'L' and resid 532 through 540 Processing helix chain 'L' and resid 572 through 576 removed outlier: 3.974A pdb=" N ARG L 576 " --> pdb=" O ALA L 573 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 68 Processing helix chain 'M' and resid 72 through 76 Processing helix chain 'M' and resid 84 through 98 Processing helix chain 'N' and resid 173 through 178 removed outlier: 3.798A pdb=" N TYR N 177 " --> pdb=" O ALA N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 187 Processing helix chain 'N' and resid 220 through 225 removed outlier: 3.711A pdb=" N THR N 224 " --> pdb=" O PRO N 220 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN N 225 " --> pdb=" O CYS N 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 220 through 225' Processing helix chain 'N' and resid 243 through 268 Processing helix chain 'N' and resid 272 through 302 removed outlier: 5.439A pdb=" N LEU N 297 " --> pdb=" O TYR N 293 " (cutoff:3.500A) Proline residue: N 298 - end of helix Processing helix chain 'N' and resid 302 through 310 Processing helix chain 'N' and resid 327 through 332 Processing helix chain 'N' and resid 333 through 338 Processing helix chain 'N' and resid 362 through 364 No H-bonds generated for 'chain 'N' and resid 362 through 364' Processing helix chain 'N' and resid 368 through 373 removed outlier: 3.510A pdb=" N VAL N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 377 through 386 Processing helix chain 'N' and resid 400 through 405 Processing helix chain 'N' and resid 416 through 428 Processing helix chain 'N' and resid 432 through 440 Processing helix chain 'N' and resid 447 through 456 Processing helix chain 'N' and resid 457 through 469 removed outlier: 3.790A pdb=" N ALA N 461 " --> pdb=" O ASN N 457 " (cutoff:3.500A) Processing helix chain 'N' and resid 470 through 474 Processing helix chain 'N' and resid 475 through 483 removed outlier: 3.532A pdb=" N GLU N 483 " --> pdb=" O GLY N 479 " (cutoff:3.500A) Processing helix chain 'N' and resid 492 through 509 Processing helix chain 'N' and resid 521 through 529 Processing helix chain 'N' and resid 532 through 540 removed outlier: 3.501A pdb=" N ASN N 540 " --> pdb=" O ILE N 536 " (cutoff:3.500A) Processing helix chain 'N' and resid 572 through 576 removed outlier: 3.794A pdb=" N ARG N 576 " --> pdb=" O ALA N 573 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 68 Processing helix chain 'O' and resid 72 through 76 Processing helix chain 'O' and resid 83 through 98 removed outlier: 3.965A pdb=" N MET O 87 " --> pdb=" O SER O 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 178 removed outlier: 3.665A pdb=" N TYR P 177 " --> pdb=" O ALA P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 188 Processing helix chain 'P' and resid 219 through 225 removed outlier: 3.749A pdb=" N ASN P 225 " --> pdb=" O CYS P 221 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 268 Processing helix chain 'P' and resid 272 through 302 removed outlier: 5.449A pdb=" N LEU P 297 " --> pdb=" O TYR P 293 " (cutoff:3.500A) Proline residue: P 298 - end of helix Processing helix chain 'P' and resid 302 through 310 Processing helix chain 'P' and resid 327 through 332 Processing helix chain 'P' and resid 333 through 339 removed outlier: 3.932A pdb=" N ILE P 339 " --> pdb=" O HIS P 336 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 364 No H-bonds generated for 'chain 'P' and resid 362 through 364' Processing helix chain 'P' and resid 368 through 373 removed outlier: 3.595A pdb=" N VAL P 372 " --> pdb=" O SER P 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 377 through 386 Processing helix chain 'P' and resid 399 through 405 Processing helix chain 'P' and resid 416 through 428 Processing helix chain 'P' and resid 432 through 440 Processing helix chain 'P' and resid 447 through 456 Processing helix chain 'P' and resid 458 through 469 Processing helix chain 'P' and resid 470 through 474 Processing helix chain 'P' and resid 475 through 483 Processing helix chain 'P' and resid 492 through 509 Processing helix chain 'P' and resid 521 through 529 Processing helix chain 'P' and resid 532 through 541 Processing helix chain 'P' and resid 572 through 576 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.072A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.187A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.685A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.284A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.352A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.513A pdb=" N ARG K 27 " --> pdb=" O ASN L 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 Processing sheet with id=AB3, first strand: chain 'K' and resid 78 through 83 removed outlier: 4.230A pdb=" N ALA L 389 " --> pdb=" O ASP K 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 188 through 189 removed outlier: 4.447A pdb=" N LEU L 196 " --> pdb=" O ASN L 189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 342 through 344 Processing sheet with id=AB6, first strand: chain 'L' and resid 546 through 547 Processing sheet with id=AB7, first strand: chain 'M' and resid 27 through 28 Processing sheet with id=AB8, first strand: chain 'M' and resid 78 through 83 removed outlier: 4.040A pdb=" N ALA N 389 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 342 through 344 Processing sheet with id=AC1, first strand: chain 'N' and resid 546 through 547 Processing sheet with id=AC2, first strand: chain 'O' and resid 27 through 28 Processing sheet with id=AC3, first strand: chain 'O' and resid 52 through 53 Processing sheet with id=AC4, first strand: chain 'P' and resid 342 through 344 Processing sheet with id=AC5, first strand: chain 'P' and resid 546 through 547 869 hydrogen bonds defined for protein. 2499 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 315 hydrogen bonds 630 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 225 stacking parallelities Total time for adding SS restraints: 5.52 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 9961 1.38 - 1.55: 15637 1.55 - 1.72: 531 1.72 - 1.89: 163 1.89 - 2.06: 12 Bond restraints: 26304 Sorted by residual: bond pdb=" C3' DA J 32 " pdb=" O3' DA J 32 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" C3' DA J -22 " pdb=" O3' DA J -22 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.85e+00 bond pdb=" C3' DA J -31 " pdb=" O3' DA J -31 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.55e+00 bond pdb=" C5 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.413 1.390 0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" C1' DC J 35 " pdb=" N1 DC J 35 " ideal model delta sigma weight residual 1.490 1.523 -0.033 3.00e-02 1.11e+03 1.18e+00 ... (remaining 26299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 36308 2.03 - 4.05: 449 4.05 - 6.08: 43 6.08 - 8.10: 2 8.10 - 10.13: 3 Bond angle restraints: 36805 Sorted by residual: angle pdb=" CB MET P 465 " pdb=" CG MET P 465 " pdb=" SD MET P 465 " ideal model delta sigma weight residual 112.70 121.46 -8.76 3.00e+00 1.11e-01 8.53e+00 angle pdb=" N ILE O 10 " pdb=" CA ILE O 10 " pdb=" C ILE O 10 " ideal model delta sigma weight residual 113.42 110.10 3.32 1.17e+00 7.31e-01 8.06e+00 angle pdb=" C ASN P 563 " pdb=" N CYS P 564 " pdb=" CA CYS P 564 " ideal model delta sigma weight residual 121.54 126.74 -5.20 1.91e+00 2.74e-01 7.42e+00 angle pdb=" CG ARG P 456 " pdb=" CD ARG P 456 " pdb=" NE ARG P 456 " ideal model delta sigma weight residual 112.00 117.59 -5.59 2.20e+00 2.07e-01 6.46e+00 angle pdb=" CB ARG P 456 " pdb=" CG ARG P 456 " pdb=" CD ARG P 456 " ideal model delta sigma weight residual 111.30 116.58 -5.28 2.30e+00 1.89e-01 5.28e+00 ... (remaining 36800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 13648 33.77 - 67.53: 1732 67.53 - 101.30: 58 101.30 - 135.06: 14 135.06 - 168.83: 7 Dihedral angle restraints: 15459 sinusoidal: 8424 harmonic: 7035 Sorted by residual: dihedral pdb=" CB CYS L 221 " pdb=" SG CYS L 221 " pdb=" SG CYS L 232 " pdb=" CB CYS L 232 " ideal model delta sinusoidal sigma weight residual -86.00 -172.35 86.35 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CA TYR P 316 " pdb=" C TYR P 316 " pdb=" N ASN P 317 " pdb=" CA ASN P 317 " ideal model delta harmonic sigma weight residual 180.00 155.19 24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA CYS L 232 " pdb=" C CYS L 232 " pdb=" N PHE L 233 " pdb=" CA PHE L 233 " ideal model delta harmonic sigma weight residual -180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 15456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3868 0.075 - 0.150: 215 0.150 - 0.225: 3 0.225 - 0.300: 0 0.300 - 0.375: 2 Chirality restraints: 4088 Sorted by residual: chirality pdb=" C1 NAG L 603 " pdb=" ND2 ASN L 189 " pdb=" C2 NAG L 603 " pdb=" O5 NAG L 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN P 317 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ASN L 189 " pdb=" N ASN L 189 " pdb=" C ASN L 189 " pdb=" CB ASN L 189 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 4085 not shown) Planarity restraints: 3823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN P 317 " 0.042 2.00e-02 2.50e+03 3.91e-02 1.92e+01 pdb=" CG ASN P 317 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN P 317 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN P 317 " -0.048 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 110 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C GLU H 110 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU H 110 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY H 111 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 111 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.48e+00 pdb=" C GLY H 111 " -0.027 2.00e-02 2.50e+03 pdb=" O GLY H 111 " 0.010 2.00e-02 2.50e+03 pdb=" N THR H 112 " 0.009 2.00e-02 2.50e+03 ... (remaining 3820 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1821 2.74 - 3.28: 23002 3.28 - 3.82: 44831 3.82 - 4.36: 53409 4.36 - 4.90: 86591 Nonbonded interactions: 209654 Sorted by model distance: nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.195 3.120 nonbonded pdb=" OH TYR L 350 " pdb=" O THR L 545 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.261 3.040 nonbonded pdb=" NH1 ARG M 62 " pdb=" OD2 ASP N 416 " model vdw 2.264 3.120 nonbonded pdb=" N GLU N 517 " pdb=" OE1 GLU N 517 " model vdw 2.270 3.120 ... (remaining 209649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 133) selection = (chain 'E' and resid 40 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = (chain 'L' and resid 121 through 603) selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.340 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 0.209 26327 Z= 0.132 Angle : 0.533 14.080 36859 Z= 0.279 Chirality : 0.037 0.375 4088 Planarity : 0.004 0.050 3818 Dihedral : 23.766 168.828 10891 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.58 % Allowed : 23.23 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.18), residues: 2396 helix: 2.12 (0.16), residues: 1161 sheet: -0.82 (0.85), residues: 36 loop : 0.05 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG P 456 TYR 0.009 0.001 TYR H 37 PHE 0.009 0.001 PHE O 86 TRP 0.008 0.001 TRP K 89 HIS 0.002 0.000 HIS P 257 Details of bonding type rmsd covalent geometry : bond 0.00305 (26304) covalent geometry : angle 0.51860 (36805) SS BOND : bond 0.00245 ( 6) SS BOND : angle 0.97939 ( 12) hydrogen bonds : bond 0.12663 ( 1184) hydrogen bonds : angle 5.18157 ( 3129) Misc. bond : bond 0.14680 ( 3) link_ALPHA1-3 : bond 0.00618 ( 1) link_ALPHA1-3 : angle 1.70258 ( 3) link_ALPHA1-6 : bond 0.00607 ( 2) link_ALPHA1-6 : angle 1.55582 ( 6) link_BETA1-4 : bond 0.00657 ( 4) link_BETA1-4 : angle 2.28799 ( 12) link_BETA1-6 : bond 0.00434 ( 2) link_BETA1-6 : angle 1.72761 ( 6) link_NAG-ASN : bond 0.00464 ( 5) link_NAG-ASN : angle 5.53897 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 276 time to evaluate : 0.873 Fit side-chains REVERT: A 42 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7716 (mmm-85) REVERT: A 56 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8090 (mtpp) REVERT: B 27 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8688 (mp10) REVERT: C 73 ASN cc_start: 0.8280 (t0) cc_final: 0.7977 (t0) REVERT: G 15 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8495 (pttp) REVERT: K 41 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: L 263 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8127 (tt0) REVERT: L 312 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8442 (m) REVERT: L 537 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.9065 (tt) REVERT: N 447 THR cc_start: 0.8881 (p) cc_final: 0.8559 (t) REVERT: O 38 GLU cc_start: 0.8625 (tt0) cc_final: 0.8224 (tt0) REVERT: O 48 THR cc_start: 0.9172 (m) cc_final: 0.8832 (p) REVERT: O 52 LYS cc_start: 0.8829 (mtmp) cc_final: 0.8503 (mttp) REVERT: O 67 GLU cc_start: 0.8603 (mp0) cc_final: 0.8125 (mp0) REVERT: O 70 ARG cc_start: 0.8833 (ttp80) cc_final: 0.8543 (ttt90) REVERT: O 80 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8377 (mp10) REVERT: P 169 SER cc_start: 0.8762 (m) cc_final: 0.8378 (p) REVERT: P 214 ASP cc_start: 0.7969 (t0) cc_final: 0.7702 (t0) REVERT: P 401 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8275 (mm-30) REVERT: P 446 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8371 (mp0) outliers start: 33 outliers final: 28 residues processed: 301 average time/residue: 0.2308 time to fit residues: 100.7323 Evaluate side-chains 304 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 41 PHE Chi-restraints excluded: chain L residue 140 GLN Chi-restraints excluded: chain L residue 221 CYS Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 362 SER Chi-restraints excluded: chain L residue 537 ILE Chi-restraints excluded: chain L residue 543 ILE Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 149 SER Chi-restraints excluded: chain N residue 238 THR Chi-restraints excluded: chain N residue 248 SER Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 540 ASN Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain P residue 174 SER Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 210 LEU Chi-restraints excluded: chain P residue 272 ASP Chi-restraints excluded: chain P residue 401 GLU Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.0670 chunk 111 optimal weight: 10.0000 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN F 25 ASN K 26 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 326 ASN M 54 ASN O 54 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.102653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.078995 restraints weight = 54380.200| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.83 r_work: 0.2987 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.274 26327 Z= 0.134 Angle : 0.534 13.093 36859 Z= 0.279 Chirality : 0.037 0.238 4088 Planarity : 0.004 0.034 3818 Dihedral : 25.229 168.756 6056 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.11 % Allowed : 21.13 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.18), residues: 2396 helix: 2.26 (0.16), residues: 1178 sheet: -0.77 (0.85), residues: 36 loop : 0.01 (0.19), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 456 TYR 0.009 0.001 TYR H 37 PHE 0.010 0.001 PHE O 86 TRP 0.007 0.001 TRP O 89 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00307 (26304) covalent geometry : angle 0.52678 (36805) SS BOND : bond 0.00397 ( 6) SS BOND : angle 0.83206 ( 12) hydrogen bonds : bond 0.04114 ( 1184) hydrogen bonds : angle 3.93095 ( 3129) Misc. bond : bond 0.17816 ( 3) link_ALPHA1-3 : bond 0.00782 ( 1) link_ALPHA1-3 : angle 2.61123 ( 3) link_ALPHA1-6 : bond 0.00897 ( 2) link_ALPHA1-6 : angle 2.03788 ( 6) link_BETA1-4 : bond 0.00520 ( 4) link_BETA1-4 : angle 2.20233 ( 12) link_BETA1-6 : bond 0.00090 ( 2) link_BETA1-6 : angle 1.39908 ( 6) link_NAG-ASN : bond 0.00607 ( 5) link_NAG-ASN : angle 3.43964 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 288 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7830 (mmm-85) REVERT: C 73 ASN cc_start: 0.8299 (t0) cc_final: 0.8032 (t0) REVERT: F 35 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8118 (mtp85) REVERT: G 15 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8546 (pttp) REVERT: K 27 ARG cc_start: 0.8810 (mmm-85) cc_final: 0.8513 (mmt90) REVERT: K 41 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: L 263 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7754 (tt0) REVERT: N 447 THR cc_start: 0.8705 (p) cc_final: 0.8502 (t) REVERT: O 38 GLU cc_start: 0.8614 (tt0) cc_final: 0.8199 (tt0) REVERT: O 48 THR cc_start: 0.9174 (m) cc_final: 0.8840 (p) REVERT: O 52 LYS cc_start: 0.8802 (mtmp) cc_final: 0.8510 (mttp) REVERT: O 66 ASN cc_start: 0.8570 (m-40) cc_final: 0.8359 (m-40) REVERT: O 67 GLU cc_start: 0.8445 (mp0) cc_final: 0.8006 (mp0) REVERT: O 70 ARG cc_start: 0.8658 (ttp80) cc_final: 0.8378 (ttt90) REVERT: P 169 SER cc_start: 0.8742 (m) cc_final: 0.8400 (p) REVERT: P 214 ASP cc_start: 0.7941 (t0) cc_final: 0.7687 (t0) REVERT: P 401 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8062 (mm-30) outliers start: 65 outliers final: 41 residues processed: 340 average time/residue: 0.2276 time to fit residues: 112.3126 Evaluate side-chains 324 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 280 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 41 PHE Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 543 ILE Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 262 THR Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 540 ASN Chi-restraints excluded: chain N residue 545 THR Chi-restraints excluded: chain N residue 566 THR Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 238 THR Chi-restraints excluded: chain P residue 377 ILE Chi-restraints excluded: chain P residue 401 GLU Chi-restraints excluded: chain P residue 545 THR Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 193 optimal weight: 0.0980 chunk 146 optimal weight: 10.0000 chunk 176 optimal weight: 0.8980 chunk 213 optimal weight: 4.9990 chunk 37 optimal weight: 0.0020 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 243 optimal weight: 0.8980 chunk 208 optimal weight: 0.0170 chunk 138 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 overall best weight: 0.3826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN K 91 GLN K 95 HIS L 201 GLN ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 326 ASN L 550 ASN M 54 ASN O 54 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.104362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.080945 restraints weight = 54552.123| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.87 r_work: 0.3022 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.220 26327 Z= 0.109 Angle : 0.505 9.889 36859 Z= 0.266 Chirality : 0.035 0.207 4088 Planarity : 0.004 0.033 3818 Dihedral : 24.920 168.999 6022 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.01 % Allowed : 21.61 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.18), residues: 2396 helix: 2.45 (0.16), residues: 1180 sheet: -0.66 (0.87), residues: 36 loop : -0.02 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 456 TYR 0.008 0.001 TYR H 37 PHE 0.009 0.001 PHE O 86 TRP 0.007 0.001 TRP L 369 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00243 (26304) covalent geometry : angle 0.49897 (36805) SS BOND : bond 0.00363 ( 6) SS BOND : angle 0.67107 ( 12) hydrogen bonds : bond 0.03492 ( 1184) hydrogen bonds : angle 3.61134 ( 3129) Misc. bond : bond 0.14247 ( 3) link_ALPHA1-3 : bond 0.01504 ( 1) link_ALPHA1-3 : angle 2.80148 ( 3) link_ALPHA1-6 : bond 0.00688 ( 2) link_ALPHA1-6 : angle 2.32788 ( 6) link_BETA1-4 : bond 0.00547 ( 4) link_BETA1-4 : angle 1.99762 ( 12) link_BETA1-6 : bond 0.00099 ( 2) link_BETA1-6 : angle 1.37553 ( 6) link_NAG-ASN : bond 0.00539 ( 5) link_NAG-ASN : angle 2.82012 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 290 time to evaluate : 0.924 Fit side-chains REVERT: C 73 ASN cc_start: 0.8293 (t0) cc_final: 0.8054 (t0) REVERT: F 35 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8178 (mtp85) REVERT: G 15 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8547 (pttp) REVERT: K 26 ASN cc_start: 0.9171 (m-40) cc_final: 0.8912 (m110) REVERT: K 27 ARG cc_start: 0.8739 (mmm-85) cc_final: 0.8503 (mmt90) REVERT: K 41 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: L 263 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7713 (tt0) REVERT: L 312 THR cc_start: 0.8373 (p) cc_final: 0.8097 (m) REVERT: L 550 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8612 (t0) REVERT: L 553 MET cc_start: 0.9004 (ttp) cc_final: 0.8668 (mtp) REVERT: M 27 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8680 (mmt90) REVERT: O 38 GLU cc_start: 0.8633 (tt0) cc_final: 0.8182 (tt0) REVERT: O 48 THR cc_start: 0.9163 (m) cc_final: 0.8836 (p) REVERT: O 52 LYS cc_start: 0.8761 (mtmp) cc_final: 0.8452 (mttp) REVERT: O 67 GLU cc_start: 0.8483 (mp0) cc_final: 0.8149 (mp0) REVERT: O 70 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8335 (ttt90) REVERT: O 80 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8317 (mp10) REVERT: P 169 SER cc_start: 0.8679 (m) cc_final: 0.8341 (p) REVERT: P 214 ASP cc_start: 0.7940 (t0) cc_final: 0.7701 (t0) outliers start: 42 outliers final: 26 residues processed: 322 average time/residue: 0.2106 time to fit residues: 98.7179 Evaluate side-chains 307 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 277 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain K residue 41 PHE Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 550 ASN Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 540 ASN Chi-restraints excluded: chain N residue 554 SER Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 117 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN F 25 ASN ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 550 ASN M 54 ASN O 54 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.096470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.072978 restraints weight = 51514.322| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.75 r_work: 0.2886 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.208 26327 Z= 0.225 Angle : 0.573 10.297 36859 Z= 0.298 Chirality : 0.039 0.184 4088 Planarity : 0.004 0.033 3818 Dihedral : 25.051 168.201 6017 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.59 % Allowed : 19.84 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.18), residues: 2396 helix: 2.21 (0.16), residues: 1181 sheet: -0.89 (0.84), residues: 36 loop : -0.16 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 456 TYR 0.011 0.001 TYR K 45 PHE 0.012 0.001 PHE O 86 TRP 0.012 0.001 TRP L 514 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00550 (26304) covalent geometry : angle 0.56646 (36805) SS BOND : bond 0.00489 ( 6) SS BOND : angle 1.28204 ( 12) hydrogen bonds : bond 0.04791 ( 1184) hydrogen bonds : angle 3.81722 ( 3129) Misc. bond : bond 0.15017 ( 3) link_ALPHA1-3 : bond 0.01818 ( 1) link_ALPHA1-3 : angle 2.25390 ( 3) link_ALPHA1-6 : bond 0.00691 ( 2) link_ALPHA1-6 : angle 2.66605 ( 6) link_BETA1-4 : bond 0.00327 ( 4) link_BETA1-4 : angle 2.59197 ( 12) link_BETA1-6 : bond 0.00240 ( 2) link_BETA1-6 : angle 1.61302 ( 6) link_NAG-ASN : bond 0.00504 ( 5) link_NAG-ASN : angle 2.96003 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 274 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7113 (mpp-170) REVERT: B 24 ASP cc_start: 0.7638 (p0) cc_final: 0.7409 (p0) REVERT: C 73 ASN cc_start: 0.8324 (t0) cc_final: 0.7984 (t0) REVERT: E 131 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.7932 (mtp85) REVERT: F 35 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8232 (mtp85) REVERT: G 15 LYS cc_start: 0.8912 (mtmt) cc_final: 0.8454 (pttp) REVERT: K 27 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8567 (mmt90) REVERT: L 263 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7703 (tt0) REVERT: O 48 THR cc_start: 0.9176 (m) cc_final: 0.8772 (p) REVERT: O 52 LYS cc_start: 0.8846 (mtmp) cc_final: 0.8515 (mttp) REVERT: O 67 GLU cc_start: 0.8534 (mp0) cc_final: 0.8075 (mp0) REVERT: O 70 ARG cc_start: 0.8718 (ttp80) cc_final: 0.8397 (ttt90) REVERT: O 80 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8369 (mp10) REVERT: P 169 SER cc_start: 0.8827 (m) cc_final: 0.8416 (p) REVERT: P 214 ASP cc_start: 0.7988 (t0) cc_final: 0.7749 (t0) REVERT: P 306 MET cc_start: 0.8699 (tpt) cc_final: 0.8497 (tpt) outliers start: 75 outliers final: 54 residues processed: 333 average time/residue: 0.2224 time to fit residues: 107.7494 Evaluate side-chains 321 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 265 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 543 ILE Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 150 CYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 262 THR Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 540 ASN Chi-restraints excluded: chain N residue 566 THR Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 238 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 377 ILE Chi-restraints excluded: chain P residue 545 THR Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 258 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 81 ASN F 25 ASN K 26 ASN ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 550 ASN M 54 ASN O 54 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.097391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.073876 restraints weight = 51605.026| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.83 r_work: 0.2888 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 26327 Z= 0.156 Angle : 0.531 9.320 36859 Z= 0.279 Chirality : 0.037 0.197 4088 Planarity : 0.004 0.036 3818 Dihedral : 24.999 167.757 6012 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.06 % Allowed : 20.46 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.18), residues: 2396 helix: 2.25 (0.16), residues: 1180 sheet: -0.80 (0.85), residues: 36 loop : -0.14 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 456 TYR 0.008 0.001 TYR L 277 PHE 0.010 0.001 PHE O 86 TRP 0.012 0.001 TRP L 514 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00373 (26304) covalent geometry : angle 0.52520 (36805) SS BOND : bond 0.00372 ( 6) SS BOND : angle 1.00737 ( 12) hydrogen bonds : bond 0.04177 ( 1184) hydrogen bonds : angle 3.68732 ( 3129) Misc. bond : bond 0.13735 ( 3) link_ALPHA1-3 : bond 0.01371 ( 1) link_ALPHA1-3 : angle 2.20357 ( 3) link_ALPHA1-6 : bond 0.01049 ( 2) link_ALPHA1-6 : angle 2.60802 ( 6) link_BETA1-4 : bond 0.00403 ( 4) link_BETA1-4 : angle 2.27423 ( 12) link_BETA1-6 : bond 0.00214 ( 2) link_BETA1-6 : angle 1.58096 ( 6) link_NAG-ASN : bond 0.00448 ( 5) link_NAG-ASN : angle 2.74464 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 272 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7107 (mpp-170) REVERT: B 24 ASP cc_start: 0.7528 (p0) cc_final: 0.7264 (p0) REVERT: C 73 ASN cc_start: 0.8283 (t0) cc_final: 0.7927 (t0) REVERT: E 131 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.7837 (mtp85) REVERT: F 35 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8066 (mtp85) REVERT: G 15 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8449 (pttp) REVERT: K 27 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.8503 (mmt90) REVERT: L 243 MET cc_start: 0.7959 (mtm) cc_final: 0.7634 (mtt) REVERT: L 263 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7723 (tt0) REVERT: L 353 MET cc_start: 0.6081 (ttp) cc_final: 0.5577 (ttp) REVERT: O 52 LYS cc_start: 0.8750 (mtmp) cc_final: 0.8440 (mttp) REVERT: O 67 GLU cc_start: 0.8353 (mp0) cc_final: 0.7875 (mp0) REVERT: O 70 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8421 (ttt180) REVERT: O 80 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8230 (mp10) REVERT: P 169 SER cc_start: 0.8692 (m) cc_final: 0.8307 (p) REVERT: P 214 ASP cc_start: 0.7864 (t0) cc_final: 0.7619 (t0) outliers start: 64 outliers final: 51 residues processed: 320 average time/residue: 0.2039 time to fit residues: 95.1370 Evaluate side-chains 321 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 268 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 543 ILE Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 150 CYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 540 ASN Chi-restraints excluded: chain N residue 566 THR Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain P residue 137 ILE Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 238 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 377 ILE Chi-restraints excluded: chain P residue 545 THR Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 115 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 228 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN F 25 ASN H 44 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 550 ASN M 54 ASN O 54 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.097110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.073623 restraints weight = 51584.753| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.81 r_work: 0.2892 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 26327 Z= 0.165 Angle : 0.538 10.059 36859 Z= 0.281 Chirality : 0.037 0.211 4088 Planarity : 0.004 0.042 3818 Dihedral : 24.949 167.419 6012 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.39 % Allowed : 20.17 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.18), residues: 2396 helix: 2.40 (0.16), residues: 1159 sheet: -0.78 (0.85), residues: 36 loop : -0.10 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG P 456 TYR 0.008 0.001 TYR L 277 PHE 0.010 0.001 PHE O 86 TRP 0.014 0.001 TRP L 514 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00397 (26304) covalent geometry : angle 0.53207 (36805) SS BOND : bond 0.00385 ( 6) SS BOND : angle 0.99427 ( 12) hydrogen bonds : bond 0.04146 ( 1184) hydrogen bonds : angle 3.65474 ( 3129) Misc. bond : bond 0.13287 ( 3) link_ALPHA1-3 : bond 0.01134 ( 1) link_ALPHA1-3 : angle 1.92630 ( 3) link_ALPHA1-6 : bond 0.01276 ( 2) link_ALPHA1-6 : angle 2.18385 ( 6) link_BETA1-4 : bond 0.00405 ( 4) link_BETA1-4 : angle 2.29054 ( 12) link_BETA1-6 : bond 0.00268 ( 2) link_BETA1-6 : angle 1.62089 ( 6) link_NAG-ASN : bond 0.00467 ( 5) link_NAG-ASN : angle 2.77183 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 270 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7089 (mpp-170) REVERT: B 24 ASP cc_start: 0.7541 (p0) cc_final: 0.7248 (p0) REVERT: C 15 LYS cc_start: 0.9074 (ptpp) cc_final: 0.8761 (mttt) REVERT: C 73 ASN cc_start: 0.8302 (t0) cc_final: 0.7920 (t0) REVERT: E 131 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.7843 (mtp85) REVERT: F 35 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8062 (mtp85) REVERT: G 15 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8410 (pttp) REVERT: K 85 MET cc_start: 0.8544 (tpp) cc_final: 0.8322 (mmt) REVERT: L 263 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7720 (tt0) REVERT: L 353 MET cc_start: 0.6075 (ttp) cc_final: 0.5567 (ttp) REVERT: O 52 LYS cc_start: 0.8751 (mtmp) cc_final: 0.8449 (mttp) REVERT: O 67 GLU cc_start: 0.8330 (mp0) cc_final: 0.7847 (mp0) REVERT: O 80 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8242 (mp10) REVERT: P 169 SER cc_start: 0.8717 (m) cc_final: 0.8329 (p) REVERT: P 401 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7900 (mm-30) outliers start: 71 outliers final: 59 residues processed: 325 average time/residue: 0.2116 time to fit residues: 100.3120 Evaluate side-chains 328 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 266 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 238 THR Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 543 ILE Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 150 CYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 262 THR Chi-restraints excluded: chain N residue 356 ASN Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 458 LEU Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 540 ASN Chi-restraints excluded: chain N residue 554 SER Chi-restraints excluded: chain N residue 564 CYS Chi-restraints excluded: chain N residue 566 THR Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain P residue 137 ILE Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 238 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 377 ILE Chi-restraints excluded: chain P residue 401 GLU Chi-restraints excluded: chain P residue 545 THR Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 212 optimal weight: 7.9990 chunk 220 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 chunk 255 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 257 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 16 optimal weight: 10.0000 chunk 250 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 81 ASN F 25 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN O 54 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.097935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.074499 restraints weight = 51229.523| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.81 r_work: 0.2905 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.202 26327 Z= 0.130 Angle : 0.523 9.377 36859 Z= 0.275 Chirality : 0.036 0.236 4088 Planarity : 0.004 0.042 3818 Dihedral : 24.913 167.297 6012 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.87 % Allowed : 20.70 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.18), residues: 2396 helix: 2.48 (0.16), residues: 1159 sheet: -0.73 (0.86), residues: 36 loop : -0.08 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG P 456 TYR 0.008 0.001 TYR H 37 PHE 0.010 0.001 PHE O 86 TRP 0.014 0.001 TRP L 514 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00304 (26304) covalent geometry : angle 0.51781 (36805) SS BOND : bond 0.00350 ( 6) SS BOND : angle 1.23682 ( 12) hydrogen bonds : bond 0.03818 ( 1184) hydrogen bonds : angle 3.58501 ( 3129) Misc. bond : bond 0.14243 ( 3) link_ALPHA1-3 : bond 0.01188 ( 1) link_ALPHA1-3 : angle 2.06655 ( 3) link_ALPHA1-6 : bond 0.01389 ( 2) link_ALPHA1-6 : angle 2.00782 ( 6) link_BETA1-4 : bond 0.00455 ( 4) link_BETA1-4 : angle 2.12658 ( 12) link_BETA1-6 : bond 0.00134 ( 2) link_BETA1-6 : angle 1.58146 ( 6) link_NAG-ASN : bond 0.00480 ( 5) link_NAG-ASN : angle 2.64727 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 267 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7539 (p0) cc_final: 0.7230 (p0) REVERT: C 15 LYS cc_start: 0.9057 (ptpp) cc_final: 0.8756 (mttt) REVERT: C 73 ASN cc_start: 0.8276 (t0) cc_final: 0.7897 (t0) REVERT: E 131 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.7814 (mtp85) REVERT: F 35 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8065 (mtp85) REVERT: G 15 LYS cc_start: 0.8866 (mtmt) cc_final: 0.8396 (pttp) REVERT: K 85 MET cc_start: 0.8531 (tpp) cc_final: 0.8323 (mmt) REVERT: L 263 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7703 (tt0) REVERT: L 353 MET cc_start: 0.6047 (ttp) cc_final: 0.5519 (ttp) REVERT: M 27 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8596 (mmt90) REVERT: M 80 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8264 (mm-40) REVERT: O 52 LYS cc_start: 0.8735 (mtmp) cc_final: 0.8434 (mttp) REVERT: O 67 GLU cc_start: 0.8337 (mp0) cc_final: 0.7870 (mp0) REVERT: O 80 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8254 (mp10) REVERT: P 169 SER cc_start: 0.8672 (m) cc_final: 0.8294 (p) outliers start: 60 outliers final: 51 residues processed: 310 average time/residue: 0.2170 time to fit residues: 97.7888 Evaluate side-chains 319 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 158 ILE Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 543 ILE Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain N residue 150 CYS Chi-restraints excluded: chain N residue 174 SER Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 191 SER Chi-restraints excluded: chain N residue 262 THR Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 564 CYS Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 238 THR Chi-restraints excluded: chain P residue 241 SER Chi-restraints excluded: chain P residue 545 THR Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 12 optimal weight: 0.8980 chunk 179 optimal weight: 0.6980 chunk 236 optimal weight: 2.9990 chunk 217 optimal weight: 0.0570 chunk 136 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 46 HIS D 81 ASN F 25 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN O 54 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.103338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.079611 restraints weight = 53985.182| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.82 r_work: 0.3012 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.204 26327 Z= 0.112 Angle : 0.507 9.107 36859 Z= 0.268 Chirality : 0.036 0.290 4088 Planarity : 0.004 0.047 3818 Dihedral : 24.778 167.695 6010 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.96 % Allowed : 21.85 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.18), residues: 2396 helix: 2.61 (0.16), residues: 1156 sheet: -0.65 (0.87), residues: 36 loop : 0.03 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG P 456 TYR 0.008 0.001 TYR H 37 PHE 0.008 0.001 PHE H 67 TRP 0.015 0.001 TRP L 514 HIS 0.005 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00254 (26304) covalent geometry : angle 0.50223 (36805) SS BOND : bond 0.00377 ( 6) SS BOND : angle 0.92417 ( 12) hydrogen bonds : bond 0.03378 ( 1184) hydrogen bonds : angle 3.45230 ( 3129) Misc. bond : bond 0.14154 ( 3) link_ALPHA1-3 : bond 0.01397 ( 1) link_ALPHA1-3 : angle 1.94073 ( 3) link_ALPHA1-6 : bond 0.01306 ( 2) link_ALPHA1-6 : angle 1.53013 ( 6) link_BETA1-4 : bond 0.00497 ( 4) link_BETA1-4 : angle 1.92817 ( 12) link_BETA1-6 : bond 0.00071 ( 2) link_BETA1-6 : angle 1.50291 ( 6) link_NAG-ASN : bond 0.00524 ( 5) link_NAG-ASN : angle 2.49551 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 277 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7575 (p0) cc_final: 0.7265 (p0) REVERT: C 15 LYS cc_start: 0.9130 (ptpp) cc_final: 0.8883 (mttt) REVERT: C 73 ASN cc_start: 0.8270 (t0) cc_final: 0.7910 (t0) REVERT: E 131 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.7824 (mtp85) REVERT: F 35 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8197 (mtp85) REVERT: G 15 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8439 (ptpp) REVERT: K 8 ARG cc_start: 0.7176 (mtt90) cc_final: 0.6869 (mtt180) REVERT: K 27 ARG cc_start: 0.9056 (mmt90) cc_final: 0.8735 (mmt90) REVERT: L 263 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7695 (tt0) REVERT: L 312 THR cc_start: 0.8442 (p) cc_final: 0.8184 (m) REVERT: M 27 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8606 (mmt90) REVERT: O 48 THR cc_start: 0.9181 (m) cc_final: 0.8826 (p) REVERT: O 52 LYS cc_start: 0.8766 (mtmp) cc_final: 0.8461 (mttp) REVERT: O 67 GLU cc_start: 0.8478 (mp0) cc_final: 0.8014 (mp0) REVERT: O 80 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8401 (mp10) REVERT: P 169 SER cc_start: 0.8731 (m) cc_final: 0.8390 (p) REVERT: P 401 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8040 (mm-30) outliers start: 41 outliers final: 32 residues processed: 307 average time/residue: 0.2248 time to fit residues: 99.8529 Evaluate side-chains 307 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 543 ILE Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 150 CYS Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 564 CYS Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 238 THR Chi-restraints excluded: chain P residue 401 GLU Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 151 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 213 optimal weight: 0.0770 chunk 161 optimal weight: 0.3980 chunk 175 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN F 25 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN O 54 ASN O 66 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.100209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.077320 restraints weight = 51347.189| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.71 r_work: 0.2985 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.207 26327 Z= 0.114 Angle : 0.506 9.422 36859 Z= 0.268 Chirality : 0.036 0.262 4088 Planarity : 0.004 0.046 3818 Dihedral : 24.759 167.835 6007 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.91 % Allowed : 22.08 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.18), residues: 2396 helix: 2.64 (0.16), residues: 1159 sheet: -0.63 (0.87), residues: 36 loop : 0.01 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG P 456 TYR 0.008 0.001 TYR H 37 PHE 0.008 0.001 PHE O 86 TRP 0.015 0.001 TRP L 514 HIS 0.003 0.000 HIS P 257 Details of bonding type rmsd covalent geometry : bond 0.00260 (26304) covalent geometry : angle 0.50120 (36805) SS BOND : bond 0.00450 ( 6) SS BOND : angle 1.14967 ( 12) hydrogen bonds : bond 0.03404 ( 1184) hydrogen bonds : angle 3.42364 ( 3129) Misc. bond : bond 0.14433 ( 3) link_ALPHA1-3 : bond 0.01279 ( 1) link_ALPHA1-3 : angle 1.76248 ( 3) link_ALPHA1-6 : bond 0.01325 ( 2) link_ALPHA1-6 : angle 1.56294 ( 6) link_BETA1-4 : bond 0.00464 ( 4) link_BETA1-4 : angle 1.96151 ( 12) link_BETA1-6 : bond 0.00082 ( 2) link_BETA1-6 : angle 1.54964 ( 6) link_NAG-ASN : bond 0.00506 ( 5) link_NAG-ASN : angle 2.46684 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 269 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7394 (p0) cc_final: 0.7114 (p0) REVERT: C 15 LYS cc_start: 0.9022 (ptpp) cc_final: 0.8795 (mttt) REVERT: C 73 ASN cc_start: 0.8187 (t0) cc_final: 0.7856 (t0) REVERT: E 131 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.7803 (mtp85) REVERT: F 35 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8054 (mtp85) REVERT: G 15 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8429 (ptpp) REVERT: K 8 ARG cc_start: 0.7210 (mtt90) cc_final: 0.6933 (mtt180) REVERT: L 263 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7675 (tt0) REVERT: L 312 THR cc_start: 0.8330 (p) cc_final: 0.8070 (m) REVERT: L 378 ASP cc_start: 0.7831 (m-30) cc_final: 0.7058 (t0) REVERT: M 27 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8549 (mmt90) REVERT: O 48 THR cc_start: 0.9186 (m) cc_final: 0.8864 (p) REVERT: O 52 LYS cc_start: 0.8686 (mtmp) cc_final: 0.8413 (mttp) REVERT: O 67 GLU cc_start: 0.8301 (mp0) cc_final: 0.7831 (mp0) REVERT: O 80 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8254 (mp10) REVERT: P 169 SER cc_start: 0.8655 (m) cc_final: 0.8323 (p) REVERT: P 401 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7952 (mm-30) outliers start: 40 outliers final: 34 residues processed: 299 average time/residue: 0.2184 time to fit residues: 94.2734 Evaluate side-chains 305 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 267 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 150 CYS Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 564 CYS Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 401 GLU Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 186 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 42 optimal weight: 0.3980 chunk 181 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 234 optimal weight: 0.6980 chunk 245 optimal weight: 6.9990 chunk 115 optimal weight: 0.0060 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN F 25 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN O 54 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.100803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.077975 restraints weight = 51584.524| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.74 r_work: 0.2971 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.206 26327 Z= 0.124 Angle : 0.514 9.678 36859 Z= 0.270 Chirality : 0.036 0.264 4088 Planarity : 0.004 0.048 3818 Dihedral : 24.764 167.717 6007 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.01 % Allowed : 22.13 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.18), residues: 2396 helix: 2.55 (0.16), residues: 1174 sheet: -0.58 (0.87), residues: 36 loop : 0.05 (0.19), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG P 456 TYR 0.008 0.001 TYR H 37 PHE 0.009 0.001 PHE O 86 TRP 0.015 0.001 TRP L 514 HIS 0.003 0.000 HIS P 257 Details of bonding type rmsd covalent geometry : bond 0.00288 (26304) covalent geometry : angle 0.50898 (36805) SS BOND : bond 0.00305 ( 6) SS BOND : angle 1.03755 ( 12) hydrogen bonds : bond 0.03546 ( 1184) hydrogen bonds : angle 3.43889 ( 3129) Misc. bond : bond 0.14573 ( 3) link_ALPHA1-3 : bond 0.01268 ( 1) link_ALPHA1-3 : angle 1.72778 ( 3) link_ALPHA1-6 : bond 0.01220 ( 2) link_ALPHA1-6 : angle 1.48672 ( 6) link_BETA1-4 : bond 0.00451 ( 4) link_BETA1-4 : angle 2.02040 ( 12) link_BETA1-6 : bond 0.00125 ( 2) link_BETA1-6 : angle 1.56698 ( 6) link_NAG-ASN : bond 0.00467 ( 5) link_NAG-ASN : angle 2.50294 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7427 (p0) cc_final: 0.7154 (p0) REVERT: C 15 LYS cc_start: 0.9020 (ptpp) cc_final: 0.8799 (mttt) REVERT: C 73 ASN cc_start: 0.8194 (t0) cc_final: 0.7861 (t0) REVERT: E 131 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.7816 (mtp85) REVERT: F 35 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8038 (mtp85) REVERT: G 15 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8414 (ptpp) REVERT: K 8 ARG cc_start: 0.7220 (mtt90) cc_final: 0.6949 (mtt180) REVERT: K 27 ARG cc_start: 0.9018 (mmt90) cc_final: 0.8687 (mmt90) REVERT: L 263 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7652 (tt0) REVERT: L 312 THR cc_start: 0.8370 (p) cc_final: 0.8125 (m) REVERT: L 378 ASP cc_start: 0.7844 (m-30) cc_final: 0.7041 (t0) REVERT: L 553 MET cc_start: 0.8965 (ttp) cc_final: 0.8644 (mtp) REVERT: M 27 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8544 (mmt90) REVERT: O 48 THR cc_start: 0.9194 (m) cc_final: 0.8860 (p) REVERT: O 52 LYS cc_start: 0.8694 (mtmp) cc_final: 0.8416 (mttp) REVERT: O 67 GLU cc_start: 0.8329 (mp0) cc_final: 0.7827 (mp0) REVERT: O 80 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8288 (mp10) REVERT: P 169 SER cc_start: 0.8688 (m) cc_final: 0.8349 (p) REVERT: P 401 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7955 (mm-30) outliers start: 42 outliers final: 36 residues processed: 297 average time/residue: 0.2213 time to fit residues: 95.0545 Evaluate side-chains 305 residues out of total 2092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 359 VAL Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 544 THR Chi-restraints excluded: chain L residue 547 SER Chi-restraints excluded: chain L residue 554 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 150 CYS Chi-restraints excluded: chain N residue 175 MET Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 526 GLN Chi-restraints excluded: chain N residue 538 CYS Chi-restraints excluded: chain N residue 564 CYS Chi-restraints excluded: chain O residue 19 SER Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain P residue 175 MET Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 192 ASN Chi-restraints excluded: chain P residue 401 GLU Chi-restraints excluded: chain P residue 564 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 112 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 259 optimal weight: 3.9990 chunk 234 optimal weight: 0.7980 chunk 233 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS F 25 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN O 54 ASN O 66 ASN ** O 91 GLN ** 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 = 0.3594 r_free = 0.3594 target = 0.099334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.076537 restraints weight = 51363.414| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.76 r_work: 0.2960 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.205 26327 Z= 0.159 Angle : 0.537 9.590 36859 Z= 0.281 Chirality : 0.037 0.265 4088 Planarity : 0.004 0.053 3818 Dihedral : 24.854 167.103 6007 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.06 % Allowed : 22.13 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.18), residues: 2396 helix: 2.47 (0.16), residues: 1174 sheet: -0.70 (0.86), residues: 36 loop : 0.01 (0.19), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG P 456 TYR 0.008 0.001 TYR H 37 PHE 0.010 0.001 PHE O 86 TRP 0.015 0.001 TRP L 514 HIS 0.005 0.001 HIS P 257 Details of bonding type rmsd covalent geometry : bond 0.00379 (26304) covalent geometry : angle 0.53177 (36805) SS BOND : bond 0.00332 ( 6) SS BOND : angle 1.12340 ( 12) hydrogen bonds : bond 0.04049 ( 1184) hydrogen bonds : angle 3.54849 ( 3129) Misc. bond : bond 0.15243 ( 3) link_ALPHA1-3 : bond 0.01097 ( 1) link_ALPHA1-3 : angle 1.52737 ( 3) link_ALPHA1-6 : bond 0.01020 ( 2) link_ALPHA1-6 : angle 1.44163 ( 6) link_BETA1-4 : bond 0.00416 ( 4) link_BETA1-4 : angle 2.21584 ( 12) link_BETA1-6 : bond 0.00217 ( 2) link_BETA1-6 : angle 1.62266 ( 6) link_NAG-ASN : bond 0.00419 ( 5) link_NAG-ASN : angle 2.62541 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6873.82 seconds wall clock time: 117 minutes 49.97 seconds (7069.97 seconds total)