Starting phenix.real_space_refine on Wed Feb 4 15:14:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9njl_49486/02_2026/9njl_49486.cif Found real_map, /net/cci-nas-00/data/ceres_data/9njl_49486/02_2026/9njl_49486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9njl_49486/02_2026/9njl_49486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9njl_49486/02_2026/9njl_49486.map" model { file = "/net/cci-nas-00/data/ceres_data/9njl_49486/02_2026/9njl_49486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9njl_49486/02_2026/9njl_49486.cif" } resolution = 2.6 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= 0.001 sd= 0.039 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 7173 2.51 5 N 1899 2.21 5 O 2190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11307 Number of models: 1 Model: "" Number of chains: 19 Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 891 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "L" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 755 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1282 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 8, 'TRANS': 163} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 670 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, '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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: I, J, N, P, C, E, D, F, M, Q, O, R Time building chain proxies: 1.81, per 1000 atoms: 0.16 Number of scatterers: 11307 At special positions: 0 Unit cell: (139.272, 135.956, 84.558, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 2190 8.00 N 1899 7.00 C 7173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 119 " distance=2.03 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 557 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.05 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.05 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 119 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 119 " distance=2.03 Simple disulfide: pdb=" SG CYS D 512 " - pdb=" SG CYS D 557 " distance=2.03 Simple disulfide: pdb=" SG CYS F 512 " - pdb=" SG CYS F 557 " 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=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN O 4 " - " MAN O 5 " " MAN R 4 " - " MAN R 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA O 3 " - " MAN O 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA K 3 " - " MAN K 6 " " BMA O 3 " - " MAN O 6 " " BMA R 3 " - " MAN R 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 301 " - " ASN A 171 " " NAG A 302 " - " ASN A 219 " " NAG A 303 " - " ASN A 202 " " NAG C 301 " - " ASN C 171 " " NAG C 302 " - " ASN C 219 " " NAG C 303 " - " ASN C 202 " " NAG E 301 " - " ASN E 171 " " NAG E 302 " - " ASN E 219 " " NAG E 303 " - " ASN E 202 " " NAG G 1 " - " ASN A 94 " " NAG K 1 " - " ASN B 564 " " NAG M 1 " - " ASN C 94 " " NAG O 1 " - " ASN D 564 " " NAG Q 1 " - " ASN E 94 " " NAG R 1 " - " ASN F 564 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 373.0 milliseconds 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 30 sheets defined 15.1% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.571A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.783A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 58 Processing helix chain 'A' and resid 62 through 68 removed outlier: 4.239A pdb=" N LYS A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 179 removed outlier: 4.130A pdb=" N MET A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 removed outlier: 4.276A pdb=" N TRP B 532 " --> pdb=" O GLY B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 577 removed outlier: 3.864A pdb=" N ALA B 567 " --> pdb=" O ALA B 563 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LYS B 568 " --> pdb=" O ASN B 564 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER B 569 " --> pdb=" O GLN B 565 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 597 removed outlier: 3.607A pdb=" N ARG B 597 " --> pdb=" O PHE B 593 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.570A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.784A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 55 through 58 Processing helix chain 'C' and resid 62 through 68 removed outlier: 4.239A pdb=" N LYS C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 179 removed outlier: 4.130A pdb=" N MET C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 533 removed outlier: 4.275A pdb=" N TRP D 532 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 577 removed outlier: 3.865A pdb=" N ALA D 567 " --> pdb=" O ALA D 563 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LYS D 568 " --> pdb=" O ASN D 564 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER D 569 " --> pdb=" O GLN D 565 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU D 571 " --> pdb=" O ALA D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 597 removed outlier: 3.607A pdb=" N ARG D 597 " --> pdb=" O PHE D 593 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.571A pdb=" N SER J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.783A pdb=" N THR J 91 " --> pdb=" O ALA J 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 58 Processing helix chain 'E' and resid 62 through 68 removed outlier: 4.239A pdb=" N LYS E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 179 removed outlier: 4.130A pdb=" N MET E 177 " --> pdb=" O THR E 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 533 removed outlier: 4.275A pdb=" N TRP F 532 " --> pdb=" O GLY F 529 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 577 removed outlier: 3.865A pdb=" N ALA F 567 " --> pdb=" O ALA F 563 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LYS F 568 " --> pdb=" O ASN F 564 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER F 569 " --> pdb=" O GLN F 565 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU F 571 " --> pdb=" O ALA F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 597 removed outlier: 3.607A pdb=" N ARG F 597 " --> pdb=" O PHE F 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.772A pdb=" N THR H 33 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.951A pdb=" N ILE H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA6, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.560A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA8, first strand: chain 'A' and resid 80 through 82 removed outlier: 5.196A pdb=" N GLU A 162 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N THR A 91 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 13.047A pdb=" N ASN A 164 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 11.178A pdb=" N ALA A 89 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS A 90 " --> pdb=" O CYS A 119 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 127 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 80 through 82 removed outlier: 7.674A pdb=" N GLU A 85 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU A 49 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLU A 87 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLY A 51 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 516 " --> pdb=" O ILE B 549 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 70 through 73 Processing sheet with id=AB2, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.772A pdb=" N THR I 33 " --> pdb=" O ARG I 99 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N MET I 34 " --> pdb=" O SER I 50 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.952A pdb=" N ILE I 109 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AB7, first strand: chain 'N' and resid 45 through 46 removed outlier: 3.560A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 48 through 49 Processing sheet with id=AB9, first strand: chain 'C' and resid 80 through 82 removed outlier: 5.196A pdb=" N GLU C 162 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N THR C 91 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 13.046A pdb=" N ASN C 164 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 11.178A pdb=" N ALA C 89 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS C 90 " --> pdb=" O CYS C 119 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY C 127 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 80 through 82 removed outlier: 7.673A pdb=" N GLU C 85 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU C 49 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLU C 87 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLY C 51 " --> pdb=" O GLU C 87 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU D 516 " --> pdb=" O ILE D 549 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AC3, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.772A pdb=" N THR J 33 " --> pdb=" O ARG J 99 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.952A pdb=" N ILE J 109 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'P' and resid 10 through 13 Processing sheet with id=AC8, first strand: chain 'P' and resid 45 through 46 removed outlier: 3.560A pdb=" N TYR P 87 " --> pdb=" O TYR P 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 48 through 49 Processing sheet with id=AD1, first strand: chain 'E' and resid 80 through 82 removed outlier: 5.196A pdb=" N GLU E 162 " --> pdb=" O THR E 91 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR E 91 " --> pdb=" O GLU E 162 " (cutoff:3.500A) removed outlier: 13.046A pdb=" N ASN E 164 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 11.178A pdb=" N ALA E 89 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS E 90 " --> pdb=" O CYS E 119 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY E 127 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 80 through 82 removed outlier: 7.674A pdb=" N GLU E 85 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU E 49 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLU E 87 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLY E 51 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU F 516 " --> pdb=" O ILE F 549 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 70 through 73 465 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3454 1.34 - 1.46: 2783 1.46 - 1.58: 5187 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 11490 Sorted by residual: bond pdb=" CG ASP H 108 " pdb=" OD2 ASP H 108 " ideal model delta sigma weight residual 1.249 1.283 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" CG ASP J 108 " pdb=" OD2 ASP J 108 " ideal model delta sigma weight residual 1.249 1.282 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" CG ASP I 108 " pdb=" OD2 ASP I 108 " ideal model delta sigma weight residual 1.249 1.282 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" C LYS P 39 " pdb=" N PRO P 40 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.12e-02 7.97e+03 2.97e+00 bond pdb=" C LYS L 39 " pdb=" N PRO L 40 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.12e-02 7.97e+03 2.86e+00 ... (remaining 11485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 14860 2.11 - 4.22: 626 4.22 - 6.33: 111 6.33 - 8.44: 41 8.44 - 10.55: 10 Bond angle restraints: 15648 Sorted by residual: angle pdb=" C LEU N 73 " pdb=" N THR N 74 " pdb=" CA THR N 74 " ideal model delta sigma weight residual 121.86 115.69 6.17 1.58e+00 4.01e-01 1.52e+01 angle pdb=" C LEU P 73 " pdb=" N THR P 74 " pdb=" CA THR P 74 " ideal model delta sigma weight residual 121.86 115.72 6.14 1.58e+00 4.01e-01 1.51e+01 angle pdb=" C LEU L 73 " pdb=" N THR L 74 " pdb=" CA THR L 74 " ideal model delta sigma weight residual 121.86 115.73 6.13 1.58e+00 4.01e-01 1.50e+01 angle pdb=" CB ARG D 558 " pdb=" CG ARG D 558 " pdb=" CD ARG D 558 " ideal model delta sigma weight residual 111.30 119.76 -8.46 2.30e+00 1.89e-01 1.35e+01 angle pdb=" CB ARG F 558 " pdb=" CG ARG F 558 " pdb=" CD ARG F 558 " ideal model delta sigma weight residual 111.30 119.74 -8.44 2.30e+00 1.89e-01 1.35e+01 ... (remaining 15643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.87: 6501 18.87 - 37.73: 513 37.73 - 56.60: 93 56.60 - 75.46: 39 75.46 - 94.33: 36 Dihedral angle restraints: 7182 sinusoidal: 3000 harmonic: 4182 Sorted by residual: dihedral pdb=" CA GLY F 506 " pdb=" C GLY F 506 " pdb=" N GLU F 507 " pdb=" CA GLU F 507 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA GLY D 506 " pdb=" C GLY D 506 " pdb=" N GLU D 507 " pdb=" CA GLU D 507 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA GLY B 506 " pdb=" C GLY B 506 " pdb=" N GLU B 507 " pdb=" CA GLU B 507 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 7179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1554 0.072 - 0.144: 294 0.144 - 0.217: 10 0.217 - 0.289: 11 0.289 - 0.361: 15 Chirality restraints: 1884 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.40e+00 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.30e+00 chirality pdb=" CG LEU B 555 " pdb=" CB LEU B 555 " pdb=" CD1 LEU B 555 " pdb=" CD2 LEU B 555 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 1881 not shown) Planarity restraints: 1959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE N 98 " 0.031 2.00e-02 2.50e+03 3.99e-02 2.78e+01 pdb=" CG PHE N 98 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 PHE N 98 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE N 98 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE N 98 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 98 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE N 98 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 98 " -0.030 2.00e-02 2.50e+03 3.99e-02 2.78e+01 pdb=" CG PHE L 98 " 0.092 2.00e-02 2.50e+03 pdb=" CD1 PHE L 98 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE L 98 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE L 98 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE L 98 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE L 98 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 98 " 0.030 2.00e-02 2.50e+03 3.98e-02 2.77e+01 pdb=" CG PHE P 98 " -0.091 2.00e-02 2.50e+03 pdb=" CD1 PHE P 98 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE P 98 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE P 98 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE P 98 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE P 98 " 0.001 2.00e-02 2.50e+03 ... (remaining 1956 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4191 2.87 - 3.38: 9368 3.38 - 3.88: 19441 3.88 - 4.39: 22826 4.39 - 4.90: 38620 Nonbonded interactions: 94446 Sorted by model distance: nonbonded pdb=" OD1 ASN E 80 " pdb=" OG SER E 151 " model vdw 2.359 3.040 nonbonded pdb=" OD1 ASN C 80 " pdb=" OG SER C 151 " model vdw 2.359 3.040 nonbonded pdb=" OD1 ASN A 80 " pdb=" OG SER A 151 " model vdw 2.360 3.040 nonbonded pdb=" OG1 THR J 33 " pdb=" OE2 GLU F 515 " model vdw 2.383 3.040 nonbonded pdb=" OG1 THR H 33 " pdb=" OE2 GLU B 515 " model vdw 2.383 3.040 ... (remaining 94441 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: 0.02 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'K' selection = chain 'O' selection = chain 'R' } 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: 7.650 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.060 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11538 Z= 0.217 Angle : 1.097 10.554 15780 Z= 0.544 Chirality : 0.062 0.361 1884 Planarity : 0.012 0.097 1944 Dihedral : 16.333 94.329 4470 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.65 % Allowed : 17.35 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.19), residues: 1419 helix: -3.03 (0.31), residues: 144 sheet: -0.77 (0.22), residues: 489 loop : -1.67 (0.18), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.003 ARG L 18 TYR 0.059 0.008 TYR P 87 PHE 0.092 0.009 PHE N 98 TRP 0.058 0.009 TRP C 198 HIS 0.046 0.012 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00479 (11490) covalent geometry : angle 1.06331 (15648) SS BOND : bond 0.00974 ( 12) SS BOND : angle 2.54973 ( 24) hydrogen bonds : bond 0.18691 ( 426) hydrogen bonds : angle 9.19462 ( 1215) link_ALPHA1-2 : bond 0.00971 ( 3) link_ALPHA1-2 : angle 2.96985 ( 9) link_ALPHA1-3 : bond 0.00556 ( 3) link_ALPHA1-3 : angle 1.56169 ( 9) link_ALPHA1-6 : bond 0.01408 ( 3) link_ALPHA1-6 : angle 2.82851 ( 9) link_BETA1-4 : bond 0.00365 ( 12) link_BETA1-4 : angle 3.69266 ( 36) link_NAG-ASN : bond 0.00716 ( 15) link_NAG-ASN : angle 3.19757 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: H 43 LYS cc_start: 0.7622 (mmtp) cc_final: 0.7253 (mppt) REVERT: H 103 ASN cc_start: 0.8186 (m110) cc_final: 0.7949 (m110) REVERT: L 45 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7869 (tptt) REVERT: A 158 LYS cc_start: 0.8839 (mmtm) cc_final: 0.8456 (mmtt) REVERT: I 3 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7490 (tt0) REVERT: I 43 LYS cc_start: 0.7597 (mmtp) cc_final: 0.7189 (mttt) REVERT: I 100 ASP cc_start: 0.8689 (t0) cc_final: 0.8357 (t0) REVERT: I 103 ASN cc_start: 0.8115 (m110) cc_final: 0.7607 (m110) REVERT: N 45 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8002 (tptt) REVERT: C 158 LYS cc_start: 0.8869 (mmtm) cc_final: 0.8540 (mmtt) REVERT: D 587 ASN cc_start: 0.8280 (m-40) cc_final: 0.7934 (m110) REVERT: J 18 LEU cc_start: 0.7349 (tp) cc_final: 0.7010 (tp) REVERT: J 43 LYS cc_start: 0.7694 (mmtp) cc_final: 0.7446 (mppt) REVERT: J 103 ASN cc_start: 0.8214 (m110) cc_final: 0.7872 (m110) REVERT: P 45 LYS cc_start: 0.8376 (ttmt) cc_final: 0.7992 (tptp) REVERT: F 587 ASN cc_start: 0.8276 (m-40) cc_final: 0.7915 (m110) REVERT: F 588 ARG cc_start: 0.8046 (tpp80) cc_final: 0.7782 (tpp80) outliers start: 27 outliers final: 8 residues processed: 201 average time/residue: 0.5719 time to fit residues: 122.9718 Evaluate side-chains 176 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain E residue 151 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 101 ASN H 103 ASN L 27 GLN A 126 GLN A 175 HIS B 587 ASN I 77 ASN I 101 ASN I 103 ASN N 27 GLN C 126 GLN C 175 HIS D 565 GLN D 587 ASN J 77 ASN J 101 ASN J 103 ASN P 27 GLN E 126 GLN E 175 HIS F 565 GLN F 587 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.189813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.162841 restraints weight = 9846.944| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.97 r_work: 0.3465 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11538 Z= 0.177 Angle : 0.703 6.668 15780 Z= 0.348 Chirality : 0.048 0.256 1884 Planarity : 0.005 0.058 1944 Dihedral : 11.260 73.888 2313 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.84 % Allowed : 14.61 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.20), residues: 1419 helix: -0.97 (0.39), residues: 162 sheet: -0.12 (0.22), residues: 498 loop : -0.94 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 72 TYR 0.018 0.002 TYR F 544 PHE 0.017 0.002 PHE N 98 TRP 0.014 0.003 TRP H 47 HIS 0.006 0.002 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00379 (11490) covalent geometry : angle 0.67673 (15648) SS BOND : bond 0.00644 ( 12) SS BOND : angle 1.39847 ( 24) hydrogen bonds : bond 0.03967 ( 426) hydrogen bonds : angle 5.78680 ( 1215) link_ALPHA1-2 : bond 0.00661 ( 3) link_ALPHA1-2 : angle 2.00763 ( 9) link_ALPHA1-3 : bond 0.01460 ( 3) link_ALPHA1-3 : angle 2.51920 ( 9) link_ALPHA1-6 : bond 0.01254 ( 3) link_ALPHA1-6 : angle 2.37422 ( 9) link_BETA1-4 : bond 0.00534 ( 12) link_BETA1-4 : angle 2.75644 ( 36) link_NAG-ASN : bond 0.00323 ( 15) link_NAG-ASN : angle 1.92448 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: H 87 ARG cc_start: 0.7009 (mtt180) cc_final: 0.6766 (mtp180) REVERT: L 45 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8138 (tptp) REVERT: A 158 LYS cc_start: 0.9070 (mmtm) cc_final: 0.8791 (mmtt) REVERT: B 515 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8462 (mt-10) REVERT: I 18 LEU cc_start: 0.8083 (tp) cc_final: 0.7847 (tp) REVERT: I 43 LYS cc_start: 0.7862 (mmtp) cc_final: 0.7539 (mttt) REVERT: N 45 LYS cc_start: 0.8736 (ttmt) cc_final: 0.8291 (tptp) REVERT: J 84 ASN cc_start: 0.8406 (m-40) cc_final: 0.8165 (m110) REVERT: P 45 LYS cc_start: 0.8634 (ttmt) cc_final: 0.8168 (tptt) outliers start: 29 outliers final: 13 residues processed: 216 average time/residue: 0.5952 time to fit residues: 137.5937 Evaluate side-chains 190 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 31 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 18 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 0.0060 overall best weight: 0.4734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN I 103 ASN D 565 GLN D 587 ASN J 77 ASN J 103 ASN P 27 GLN F 565 GLN F 587 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.187387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.163221 restraints weight = 10025.141| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.43 r_work: 0.3416 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11538 Z= 0.147 Angle : 0.672 8.325 15780 Z= 0.325 Chirality : 0.047 0.212 1884 Planarity : 0.004 0.042 1944 Dihedral : 9.328 66.202 2298 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.84 % Allowed : 14.71 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.21), residues: 1419 helix: -0.07 (0.40), residues: 177 sheet: 0.07 (0.22), residues: 498 loop : -0.64 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 19 TYR 0.010 0.002 TYR A 146 PHE 0.012 0.002 PHE E 144 TRP 0.014 0.002 TRP I 47 HIS 0.005 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00307 (11490) covalent geometry : angle 0.64109 (15648) SS BOND : bond 0.00789 ( 12) SS BOND : angle 1.16289 ( 24) hydrogen bonds : bond 0.03665 ( 426) hydrogen bonds : angle 5.40185 ( 1215) link_ALPHA1-2 : bond 0.00528 ( 3) link_ALPHA1-2 : angle 1.78101 ( 9) link_ALPHA1-3 : bond 0.01274 ( 3) link_ALPHA1-3 : angle 2.15723 ( 9) link_ALPHA1-6 : bond 0.01517 ( 3) link_ALPHA1-6 : angle 2.40299 ( 9) link_BETA1-4 : bond 0.00461 ( 12) link_BETA1-4 : angle 2.58737 ( 36) link_NAG-ASN : bond 0.00581 ( 15) link_NAG-ASN : angle 2.59858 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8055 (tp) cc_final: 0.7848 (tp) REVERT: H 43 LYS cc_start: 0.7770 (mppt) cc_final: 0.7488 (mptt) REVERT: H 84 ASN cc_start: 0.8472 (m-40) cc_final: 0.8258 (m110) REVERT: H 100 ASP cc_start: 0.8959 (t0) cc_final: 0.8740 (t0) REVERT: L 34 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8704 (m110) REVERT: L 45 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8095 (tptt) REVERT: A 216 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7844 (tm-30) REVERT: B 558 ARG cc_start: 0.8171 (mtm180) cc_final: 0.7907 (mtp180) REVERT: B 564 ASN cc_start: 0.8963 (t0) cc_final: 0.8690 (t0) REVERT: I 43 LYS cc_start: 0.7889 (mmtp) cc_final: 0.7504 (mttt) REVERT: N 45 LYS cc_start: 0.8720 (ttmt) cc_final: 0.8234 (tptp) REVERT: N 61 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6215 (ptt-90) REVERT: P 45 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8118 (tptt) REVERT: E 126 GLN cc_start: 0.7593 (tt0) cc_final: 0.7021 (mt0) outliers start: 29 outliers final: 14 residues processed: 204 average time/residue: 0.6359 time to fit residues: 138.3370 Evaluate side-chains 200 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 569 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 0.0670 chunk 103 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 101 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN B 587 ASN I 103 ASN D 565 GLN D 587 ASN J 77 ASN J 103 ASN P 27 GLN F 587 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.185780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3613 r_free = 0.3613 target = 0.156973 restraints weight = 10035.172| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.06 r_work: 0.3383 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11538 Z= 0.166 Angle : 0.666 8.576 15780 Z= 0.326 Chirality : 0.047 0.228 1884 Planarity : 0.004 0.041 1944 Dihedral : 8.236 59.658 2296 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.84 % Allowed : 13.73 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1419 helix: 0.51 (0.41), residues: 177 sheet: 0.30 (0.23), residues: 495 loop : -0.46 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 19 TYR 0.027 0.002 TYR A 218 PHE 0.013 0.002 PHE E 144 TRP 0.013 0.002 TRP I 47 HIS 0.004 0.001 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00349 (11490) covalent geometry : angle 0.63469 (15648) SS BOND : bond 0.01105 ( 12) SS BOND : angle 0.82114 ( 24) hydrogen bonds : bond 0.03657 ( 426) hydrogen bonds : angle 5.24357 ( 1215) link_ALPHA1-2 : bond 0.00533 ( 3) link_ALPHA1-2 : angle 1.65800 ( 9) link_ALPHA1-3 : bond 0.01371 ( 3) link_ALPHA1-3 : angle 2.19423 ( 9) link_ALPHA1-6 : bond 0.01639 ( 3) link_ALPHA1-6 : angle 2.58210 ( 9) link_BETA1-4 : bond 0.00438 ( 12) link_BETA1-4 : angle 2.47537 ( 36) link_NAG-ASN : bond 0.00369 ( 15) link_NAG-ASN : angle 2.68144 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7877 (mppt) cc_final: 0.7634 (mptt) REVERT: H 84 ASN cc_start: 0.8638 (m-40) cc_final: 0.8383 (m110) REVERT: L 45 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8163 (tmtm) REVERT: A 126 GLN cc_start: 0.7680 (tt0) cc_final: 0.7268 (mt0) REVERT: A 216 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7858 (tm-30) REVERT: B 558 ARG cc_start: 0.8251 (mtm180) cc_final: 0.7979 (mtp180) REVERT: B 564 ASN cc_start: 0.8996 (t0) cc_final: 0.8764 (t0) REVERT: I 43 LYS cc_start: 0.7880 (mmtp) cc_final: 0.7542 (mttt) REVERT: I 103 ASN cc_start: 0.8454 (m-40) cc_final: 0.8188 (m110) REVERT: N 45 LYS cc_start: 0.8766 (ttmt) cc_final: 0.8296 (tptp) REVERT: C 126 GLN cc_start: 0.7781 (tt0) cc_final: 0.7291 (mt0) REVERT: D 515 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8680 (mt-10) REVERT: J 84 ASN cc_start: 0.8505 (m-40) cc_final: 0.8299 (m110) REVERT: P 45 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8202 (tptt) REVERT: E 126 GLN cc_start: 0.7548 (tt0) cc_final: 0.7131 (mt0) outliers start: 29 outliers final: 21 residues processed: 209 average time/residue: 0.6180 time to fit residues: 137.9833 Evaluate side-chains 209 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 569 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 130 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN B 587 ASN D 565 GLN D 587 ASN J 103 ASN P 27 GLN F 587 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.184451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.160255 restraints weight = 9963.496| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.45 r_work: 0.3352 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11538 Z= 0.187 Angle : 0.671 10.633 15780 Z= 0.331 Chirality : 0.047 0.233 1884 Planarity : 0.004 0.040 1944 Dihedral : 7.742 54.971 2296 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.43 % Allowed : 13.82 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.21), residues: 1419 helix: 0.83 (0.43), residues: 177 sheet: 0.41 (0.23), residues: 492 loop : -0.48 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.015 0.002 TYR A 218 PHE 0.014 0.002 PHE E 144 TRP 0.013 0.002 TRP I 47 HIS 0.004 0.001 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00403 (11490) covalent geometry : angle 0.64063 (15648) SS BOND : bond 0.01254 ( 12) SS BOND : angle 0.84512 ( 24) hydrogen bonds : bond 0.03771 ( 426) hydrogen bonds : angle 5.26352 ( 1215) link_ALPHA1-2 : bond 0.00511 ( 3) link_ALPHA1-2 : angle 1.57189 ( 9) link_ALPHA1-3 : bond 0.01347 ( 3) link_ALPHA1-3 : angle 2.11218 ( 9) link_ALPHA1-6 : bond 0.01778 ( 3) link_ALPHA1-6 : angle 2.71282 ( 9) link_BETA1-4 : bond 0.00392 ( 12) link_BETA1-4 : angle 2.33416 ( 36) link_NAG-ASN : bond 0.00437 ( 15) link_NAG-ASN : angle 2.71141 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7912 (mppt) cc_final: 0.7708 (mptt) REVERT: H 84 ASN cc_start: 0.8624 (m-40) cc_final: 0.8413 (m110) REVERT: L 45 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8216 (tmtm) REVERT: A 126 GLN cc_start: 0.7757 (tt0) cc_final: 0.7300 (mp10) REVERT: B 558 ARG cc_start: 0.8255 (mtm180) cc_final: 0.8048 (mtp180) REVERT: I 43 LYS cc_start: 0.7893 (mmtp) cc_final: 0.7571 (mptt) REVERT: I 100 ASP cc_start: 0.9044 (t0) cc_final: 0.8576 (t0) REVERT: I 103 ASN cc_start: 0.8549 (m-40) cc_final: 0.8107 (m110) REVERT: N 45 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8311 (tptp) REVERT: C 126 GLN cc_start: 0.7723 (tt0) cc_final: 0.7265 (mt0) REVERT: P 45 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8212 (tptt) REVERT: E 126 GLN cc_start: 0.7592 (tt0) cc_final: 0.7164 (mt0) outliers start: 35 outliers final: 25 residues processed: 213 average time/residue: 0.5925 time to fit residues: 135.3279 Evaluate side-chains 210 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 569 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 99 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 74 optimal weight: 0.0470 chunk 112 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN L 34 ASN B 587 ASN D 565 GLN D 587 ASN J 103 ASN P 27 GLN F 587 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.184967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3676 r_free = 0.3676 target = 0.162657 restraints weight = 10019.660| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.32 r_work: 0.3393 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11538 Z= 0.158 Angle : 0.637 9.946 15780 Z= 0.314 Chirality : 0.046 0.230 1884 Planarity : 0.004 0.038 1944 Dihedral : 7.417 51.632 2296 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.75 % Allowed : 14.22 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1419 helix: 1.00 (0.43), residues: 177 sheet: 0.49 (0.23), residues: 492 loop : -0.38 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.015 0.002 TYR F 544 PHE 0.010 0.001 PHE E 144 TRP 0.012 0.002 TRP I 47 HIS 0.003 0.001 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00333 (11490) covalent geometry : angle 0.60963 (15648) SS BOND : bond 0.01050 ( 12) SS BOND : angle 0.76899 ( 24) hydrogen bonds : bond 0.03509 ( 426) hydrogen bonds : angle 5.12196 ( 1215) link_ALPHA1-2 : bond 0.00511 ( 3) link_ALPHA1-2 : angle 1.50818 ( 9) link_ALPHA1-3 : bond 0.01383 ( 3) link_ALPHA1-3 : angle 2.07537 ( 9) link_ALPHA1-6 : bond 0.01902 ( 3) link_ALPHA1-6 : angle 2.77112 ( 9) link_BETA1-4 : bond 0.00373 ( 12) link_BETA1-4 : angle 2.13314 ( 36) link_NAG-ASN : bond 0.00360 ( 15) link_NAG-ASN : angle 2.53542 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 84 ASN cc_start: 0.8586 (m-40) cc_final: 0.8377 (m110) REVERT: L 45 LYS cc_start: 0.8624 (ttmt) cc_final: 0.8173 (tmtm) REVERT: A 126 GLN cc_start: 0.7755 (tt0) cc_final: 0.7326 (mp10) REVERT: A 158 LYS cc_start: 0.9084 (mmtm) cc_final: 0.8805 (mmtt) REVERT: B 558 ARG cc_start: 0.8240 (mtm180) cc_final: 0.8030 (mtp180) REVERT: I 43 LYS cc_start: 0.7907 (mmtp) cc_final: 0.7570 (mptt) REVERT: I 100 ASP cc_start: 0.9014 (t0) cc_final: 0.8688 (t0) REVERT: I 103 ASN cc_start: 0.8479 (m-40) cc_final: 0.8274 (m110) REVERT: N 45 LYS cc_start: 0.8726 (ttmt) cc_final: 0.8240 (tptt) REVERT: C 126 GLN cc_start: 0.7733 (tt0) cc_final: 0.7291 (mt0) REVERT: C 158 LYS cc_start: 0.9104 (mmtm) cc_final: 0.8795 (mmtt) REVERT: P 45 LYS cc_start: 0.8681 (ttmt) cc_final: 0.8184 (tmtm) REVERT: E 126 GLN cc_start: 0.7554 (tt0) cc_final: 0.7187 (mt0) outliers start: 28 outliers final: 21 residues processed: 209 average time/residue: 0.6595 time to fit residues: 146.9469 Evaluate side-chains 210 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 569 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 66 optimal weight: 0.4980 chunk 86 optimal weight: 0.0270 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 1 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 587 ASN D 565 GLN D 587 ASN J 103 ASN P 27 GLN F 587 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.182950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.159611 restraints weight = 9957.617| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.39 r_work: 0.3376 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11538 Z= 0.224 Angle : 0.706 8.451 15780 Z= 0.350 Chirality : 0.048 0.243 1884 Planarity : 0.005 0.048 1944 Dihedral : 7.442 48.590 2296 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.84 % Allowed : 14.71 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.22), residues: 1419 helix: 1.00 (0.43), residues: 177 sheet: 0.42 (0.23), residues: 492 loop : -0.39 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 99 TYR 0.014 0.003 TYR C 116 PHE 0.016 0.002 PHE E 144 TRP 0.011 0.002 TRP I 47 HIS 0.004 0.001 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00488 (11490) covalent geometry : angle 0.68087 (15648) SS BOND : bond 0.01519 ( 12) SS BOND : angle 0.93218 ( 24) hydrogen bonds : bond 0.03998 ( 426) hydrogen bonds : angle 5.37036 ( 1215) link_ALPHA1-2 : bond 0.00511 ( 3) link_ALPHA1-2 : angle 1.48406 ( 9) link_ALPHA1-3 : bond 0.01304 ( 3) link_ALPHA1-3 : angle 2.10542 ( 9) link_ALPHA1-6 : bond 0.01903 ( 3) link_ALPHA1-6 : angle 2.86550 ( 9) link_BETA1-4 : bond 0.00383 ( 12) link_BETA1-4 : angle 2.21931 ( 36) link_NAG-ASN : bond 0.00516 ( 15) link_NAG-ASN : angle 2.44877 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8248 (tmtm) REVERT: A 126 GLN cc_start: 0.7797 (tt0) cc_final: 0.7454 (mp10) REVERT: B 558 ARG cc_start: 0.8330 (mtm180) cc_final: 0.8110 (mtp180) REVERT: I 43 LYS cc_start: 0.7928 (mmtp) cc_final: 0.7605 (mptt) REVERT: I 100 ASP cc_start: 0.9032 (t0) cc_final: 0.8739 (t0) REVERT: N 45 LYS cc_start: 0.8772 (ttmt) cc_final: 0.8320 (tptt) REVERT: C 126 GLN cc_start: 0.7686 (tt0) cc_final: 0.7356 (mt0) REVERT: C 158 LYS cc_start: 0.9142 (mmtm) cc_final: 0.8844 (mmtt) REVERT: P 45 LYS cc_start: 0.8674 (ttmt) cc_final: 0.8241 (tmtm) REVERT: E 126 GLN cc_start: 0.7508 (tt0) cc_final: 0.7250 (mt0) outliers start: 29 outliers final: 22 residues processed: 213 average time/residue: 0.5922 time to fit residues: 134.7070 Evaluate side-chains 211 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 569 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 12 optimal weight: 3.9990 chunk 96 optimal weight: 0.3980 chunk 127 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN B 587 ASN I 103 ASN D 565 GLN D 587 ASN J 103 ASN P 27 GLN F 587 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.184845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.169853 restraints weight = 9941.849| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 0.58 r_work: 0.3590 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11538 Z= 0.150 Angle : 0.619 7.065 15780 Z= 0.307 Chirality : 0.045 0.233 1884 Planarity : 0.004 0.037 1944 Dihedral : 7.082 46.373 2296 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.84 % Allowed : 15.29 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.22), residues: 1419 helix: 1.11 (0.44), residues: 177 sheet: 0.53 (0.23), residues: 489 loop : -0.30 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 61 TYR 0.016 0.002 TYR F 544 PHE 0.008 0.001 PHE F 593 TRP 0.012 0.002 TRP I 47 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00319 (11490) covalent geometry : angle 0.59499 (15648) SS BOND : bond 0.00997 ( 12) SS BOND : angle 0.75611 ( 24) hydrogen bonds : bond 0.03425 ( 426) hydrogen bonds : angle 5.08720 ( 1215) link_ALPHA1-2 : bond 0.00518 ( 3) link_ALPHA1-2 : angle 1.40930 ( 9) link_ALPHA1-3 : bond 0.01345 ( 3) link_ALPHA1-3 : angle 1.99501 ( 9) link_ALPHA1-6 : bond 0.02034 ( 3) link_ALPHA1-6 : angle 2.87435 ( 9) link_BETA1-4 : bond 0.00350 ( 12) link_BETA1-4 : angle 1.99842 ( 36) link_NAG-ASN : bond 0.00307 ( 15) link_NAG-ASN : angle 2.20193 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 45 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8167 (tmtm) REVERT: N 45 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8286 (tptt) REVERT: C 158 LYS cc_start: 0.9080 (mmtm) cc_final: 0.8870 (mmtt) REVERT: P 45 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8207 (tmtm) outliers start: 29 outliers final: 23 residues processed: 212 average time/residue: 0.6039 time to fit residues: 136.3888 Evaluate side-chains 210 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 569 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 136 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 587 ASN I 103 ASN D 565 GLN D 587 ASN J 103 ASN F 587 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.182915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.156437 restraints weight = 9962.107| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.83 r_work: 0.3368 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11538 Z= 0.210 Angle : 0.687 8.251 15780 Z= 0.342 Chirality : 0.048 0.240 1884 Planarity : 0.005 0.045 1944 Dihedral : 7.248 48.841 2296 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.04 % Allowed : 15.88 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.22), residues: 1419 helix: 1.09 (0.44), residues: 177 sheet: 0.39 (0.23), residues: 495 loop : -0.35 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 558 TYR 0.012 0.003 TYR C 116 PHE 0.014 0.002 PHE E 144 TRP 0.012 0.002 TRP I 47 HIS 0.004 0.001 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00458 (11490) covalent geometry : angle 0.66455 (15648) SS BOND : bond 0.01471 ( 12) SS BOND : angle 0.91466 ( 24) hydrogen bonds : bond 0.03880 ( 426) hydrogen bonds : angle 5.30549 ( 1215) link_ALPHA1-2 : bond 0.00511 ( 3) link_ALPHA1-2 : angle 1.40812 ( 9) link_ALPHA1-3 : bond 0.01260 ( 3) link_ALPHA1-3 : angle 2.03795 ( 9) link_ALPHA1-6 : bond 0.02000 ( 3) link_ALPHA1-6 : angle 2.88693 ( 9) link_BETA1-4 : bond 0.00367 ( 12) link_BETA1-4 : angle 2.14165 ( 36) link_NAG-ASN : bond 0.00452 ( 15) link_NAG-ASN : angle 2.26913 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7782 (mptt) cc_final: 0.6997 (ptmm) REVERT: L 45 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8243 (tmtm) REVERT: N 45 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8318 (tptt) REVERT: C 158 LYS cc_start: 0.9116 (mmtm) cc_final: 0.8825 (mmtt) REVERT: P 45 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8253 (tmtm) outliers start: 31 outliers final: 24 residues processed: 207 average time/residue: 0.6647 time to fit residues: 146.3955 Evaluate side-chains 207 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 569 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 60 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 81 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN B 587 ASN I 103 ASN D 565 GLN D 587 ASN J 103 ASN F 587 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.184191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.160512 restraints weight = 9976.356| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.52 r_work: 0.3408 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11538 Z= 0.162 Angle : 0.631 7.339 15780 Z= 0.314 Chirality : 0.046 0.232 1884 Planarity : 0.004 0.038 1944 Dihedral : 7.095 54.504 2296 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.65 % Allowed : 16.18 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.22), residues: 1419 helix: 1.13 (0.44), residues: 177 sheet: 0.48 (0.23), residues: 489 loop : -0.29 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 61 TYR 0.012 0.002 TYR I 95 PHE 0.009 0.002 PHE E 144 TRP 0.012 0.002 TRP I 47 HIS 0.003 0.001 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00347 (11490) covalent geometry : angle 0.60864 (15648) SS BOND : bond 0.01101 ( 12) SS BOND : angle 0.79673 ( 24) hydrogen bonds : bond 0.03504 ( 426) hydrogen bonds : angle 5.13443 ( 1215) link_ALPHA1-2 : bond 0.00520 ( 3) link_ALPHA1-2 : angle 1.35711 ( 9) link_ALPHA1-3 : bond 0.01309 ( 3) link_ALPHA1-3 : angle 1.97339 ( 9) link_ALPHA1-6 : bond 0.02090 ( 3) link_ALPHA1-6 : angle 2.89270 ( 9) link_BETA1-4 : bond 0.00347 ( 12) link_BETA1-4 : angle 2.00755 ( 36) link_NAG-ASN : bond 0.00327 ( 15) link_NAG-ASN : angle 2.13748 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7683 (mptt) cc_final: 0.6923 (ptmm) REVERT: L 45 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8212 (tmtm) REVERT: A 85 GLU cc_start: 0.9012 (pm20) cc_final: 0.8704 (pp20) REVERT: B 515 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8322 (mt-10) REVERT: B 558 ARG cc_start: 0.8249 (mtm180) cc_final: 0.8047 (mtp180) REVERT: N 45 LYS cc_start: 0.8766 (ttmt) cc_final: 0.8309 (tptt) REVERT: C 158 LYS cc_start: 0.9106 (mmtm) cc_final: 0.8827 (mmtt) REVERT: P 45 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8253 (tmtm) outliers start: 27 outliers final: 24 residues processed: 208 average time/residue: 0.6180 time to fit residues: 137.1962 Evaluate side-chains 212 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain P residue 22 THR Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 569 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 74 optimal weight: 0.0060 chunk 20 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN B 587 ASN I 103 ASN D 565 GLN D 587 ASN J 103 ASN F 587 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.185663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.161533 restraints weight = 10126.983| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.32 r_work: 0.3383 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11538 Z= 0.124 Angle : 0.586 7.189 15780 Z= 0.291 Chirality : 0.044 0.237 1884 Planarity : 0.004 0.037 1944 Dihedral : 6.907 59.976 2296 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.35 % Allowed : 16.47 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.22), residues: 1419 helix: 1.24 (0.44), residues: 177 sheet: 0.53 (0.23), residues: 489 loop : -0.18 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 61 TYR 0.015 0.001 TYR F 544 PHE 0.010 0.001 PHE F 583 TRP 0.012 0.001 TRP I 102 HIS 0.002 0.001 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00260 (11490) covalent geometry : angle 0.56423 (15648) SS BOND : bond 0.00797 ( 12) SS BOND : angle 0.70426 ( 24) hydrogen bonds : bond 0.03137 ( 426) hydrogen bonds : angle 4.92802 ( 1215) link_ALPHA1-2 : bond 0.00528 ( 3) link_ALPHA1-2 : angle 1.32687 ( 9) link_ALPHA1-3 : bond 0.01306 ( 3) link_ALPHA1-3 : angle 1.88920 ( 9) link_ALPHA1-6 : bond 0.02151 ( 3) link_ALPHA1-6 : angle 2.85504 ( 9) link_BETA1-4 : bond 0.00369 ( 12) link_BETA1-4 : angle 1.92823 ( 36) link_NAG-ASN : bond 0.00261 ( 15) link_NAG-ASN : angle 1.97714 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4454.65 seconds wall clock time: 76 minutes 29.79 seconds (4589.79 seconds total)