Starting phenix.real_space_refine on Mon Aug 25 23:51:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgv_41245/08_2025/8tgv_41245_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgv_41245/08_2025/8tgv_41245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tgv_41245/08_2025/8tgv_41245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgv_41245/08_2025/8tgv_41245.map" model { file = "/net/cci-nas-00/data/ceres_data/8tgv_41245/08_2025/8tgv_41245_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgv_41245/08_2025/8tgv_41245_trim.cif" } resolution = 3.75 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= -0.000 sd= 0.044 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: 5 Type Number sf(0) Gaussians S 108 5.16 5 C 10406 2.51 5 N 2785 2.21 5 O 3221 1.98 5 H 15140 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31660 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 2998 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 198} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'ARG:plan': 5, 'GLU:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 85 Chain: "E" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3091 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 197} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "F" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3151 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 2176 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 156} Chain breaks: 5 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3040 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 199} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3130 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2223 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 153} Chain breaks: 5 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 4, 'HIS:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 85 Chain: "I" Number of atoms: 3084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3084 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3132 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 2709 Classifications: {'peptide': 192} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 177} Chain breaks: 3 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "L" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 2789 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "Z" 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.75, per 1000 atoms: 0.21 Number of scatterers: 31660 At special positions: 0 Unit cell: (124.95, 160.65, 174.037, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 O 3221 8.00 N 2785 7.00 C 10406 6.00 H 15140 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 452 " - pdb=" SG CYS A 620 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 564 " distance=2.03 Simple disulfide: pdb=" SG CYS A 508 " - pdb=" SG CYS A 552 " distance=2.04 Simple disulfide: pdb=" SG CYS A 569 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 581 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 607 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 503 " distance=2.03 Simple disulfide: pdb=" SG CYS D 452 " - pdb=" SG CYS D 620 " distance=2.03 Simple disulfide: pdb=" SG CYS D 459 " - pdb=" SG CYS D 486 " distance=2.03 Simple disulfide: pdb=" SG CYS D 494 " - pdb=" SG CYS D 564 " distance=2.03 Simple disulfide: pdb=" SG CYS D 508 " - pdb=" SG CYS D 552 " distance=2.03 Simple disulfide: pdb=" SG CYS D 569 " - pdb=" SG CYS D 597 " distance=2.03 Simple disulfide: pdb=" SG CYS D 607 " - pdb=" SG CYS D 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 193 " distance=2.03 Simple disulfide: pdb=" SG CYS G 429 " - pdb=" SG CYS G 503 " distance=2.03 Simple disulfide: pdb=" SG CYS G 452 " - pdb=" SG CYS G 620 " distance=2.03 Simple disulfide: pdb=" SG CYS G 459 " - pdb=" SG CYS G 486 " distance=2.03 Simple disulfide: pdb=" SG CYS G 494 " - pdb=" SG CYS G 564 " distance=2.03 Simple disulfide: pdb=" SG CYS G 508 " - pdb=" SG CYS G 552 " distance=2.04 Simple disulfide: pdb=" SG CYS G 569 " - pdb=" SG CYS G 597 " distance=2.03 Simple disulfide: pdb=" SG CYS G 581 " - pdb=" SG CYS G 585 " distance=2.03 Simple disulfide: pdb=" SG CYS G 607 " - pdb=" SG CYS G 644 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 145 " - pdb=" SG CYS I 201 " distance=2.03 Simple disulfide: pdb=" SG CYS I 221 " - pdb=" SG CYS L 213 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 87 " distance=2.04 Simple disulfide: pdb=" SG CYS J 133 " - pdb=" SG CYS J 193 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 145 " - pdb=" SG CYS K 201 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.04 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 BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG A 701 " - " ASN A 540 " " NAG H 1 " - " ASN A 556 " " NAG M 1 " - " ASN D 423 " " NAG N 1 " - " ASN G 423 " " NAG Z 1 " - " ASN A 423 " Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4096 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 51 sheets defined 9.3% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.951A pdb=" N PHE A 442 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 removed outlier: 3.926A pdb=" N ARG A 455 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 619 through 622 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 190 through 194 Processing helix chain 'F' and resid 26 through 30 removed outlier: 3.507A pdb=" N LYS F 30 " --> pdb=" O LEU F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 removed outlier: 4.075A pdb=" N GLU F 82 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 127 Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'D' and resid 437 through 441 Processing helix chain 'D' and resid 451 through 457 removed outlier: 4.019A pdb=" N ARG D 455 " --> pdb=" O GLY D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 547 Processing helix chain 'D' and resid 613 through 618 removed outlier: 3.613A pdb=" N HIS D 617 " --> pdb=" O TYR D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 622 removed outlier: 3.694A pdb=" N VAL D 622 " --> pdb=" O PRO D 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 619 through 622' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 190 through 196 removed outlier: 3.627A pdb=" N GLY B 195 " --> pdb=" O SER B 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 30 removed outlier: 3.579A pdb=" N ASP C 29 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 removed outlier: 4.006A pdb=" N LEU C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 125' Processing helix chain 'G' and resid 438 through 442 removed outlier: 4.281A pdb=" N PHE G 442 " --> pdb=" O ALA G 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 457 removed outlier: 3.872A pdb=" N ARG G 455 " --> pdb=" O GLY G 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 500 through 502 No H-bonds generated for 'chain 'G' and resid 500 through 502' Processing helix chain 'G' and resid 543 through 547 Processing helix chain 'G' and resid 594 through 598 Processing helix chain 'G' and resid 613 through 618 Processing helix chain 'G' and resid 619 through 622 removed outlier: 3.743A pdb=" N VAL G 622 " --> pdb=" O PRO G 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 619 through 622' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 161 through 163 No H-bonds generated for 'chain 'I' and resid 161 through 163' Processing helix chain 'I' and resid 192 through 194 No H-bonds generated for 'chain 'I' and resid 192 through 194' Processing helix chain 'I' and resid 206 through 209 Processing helix chain 'J' and resid 26 through 30 Processing helix chain 'J' and resid 78 through 82 Processing helix chain 'J' and resid 123 through 126 Processing helix chain 'J' and resid 182 through 186 removed outlier: 3.592A pdb=" N GLU J 186 " --> pdb=" O LYS J 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 182 through 186' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.794A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 163 No H-bonds generated for 'chain 'K' and resid 161 through 163' Processing helix chain 'K' and resid 192 through 194 No H-bonds generated for 'chain 'K' and resid 192 through 194' Processing helix chain 'K' and resid 206 through 209 Processing helix chain 'L' and resid 122 through 126 Processing sheet with id=AA1, first strand: chain 'A' and resid 496 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 513 through 515 removed outlier: 4.132A pdb=" N TYR A 507 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR A 553 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 509 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLY A 551 " --> pdb=" O PHE A 509 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 602 through 604 removed outlier: 7.357A pdb=" N TRP A 602 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL A 609 " --> pdb=" O TRP A 602 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 604 " --> pdb=" O CYS A 607 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 17 through 23 Processing sheet with id=AA5, first strand: chain 'E' and resid 55 through 60 removed outlier: 5.088A pdb=" N THR E 57 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE E 52 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET E 59 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET E 48 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 55 through 60 removed outlier: 5.088A pdb=" N THR E 57 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE E 52 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET E 59 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET E 48 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 125 through 128 removed outlier: 3.592A pdb=" N SER E 185 " --> pdb=" O CYS E 145 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 141 through 142 Processing sheet with id=AA9, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.507A pdb=" N LYS E 214 " --> pdb=" O CYS E 201 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.518A pdb=" N THR F 101 " --> pdb=" O TYR F 85 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP F 34 " --> pdb=" O VAL F 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.518A pdb=" N THR F 101 " --> pdb=" O TYR F 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'F' and resid 113 through 117 removed outlier: 3.652A pdb=" N SER F 113 " --> pdb=" O ASN F 136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN F 136 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL F 132 " --> pdb=" O PHE F 117 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F 129 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR F 172 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 144 through 149 Processing sheet with id=AB6, first strand: chain 'F' and resid 144 through 149 Processing sheet with id=AB7, first strand: chain 'D' and resid 513 through 516 removed outlier: 3.516A pdb=" N VAL D 516 " --> pdb=" O VAL D 506 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL D 506 " --> pdb=" O VAL D 516 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR D 507 " --> pdb=" O THR D 553 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR D 553 " --> pdb=" O TYR D 507 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE D 509 " --> pdb=" O GLY D 551 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY D 551 " --> pdb=" O PHE D 509 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 562 " --> pdb=" O TRP D 554 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 602 through 604 removed outlier: 7.577A pdb=" N TRP D 602 " --> pdb=" O VAL D 609 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL D 609 " --> pdb=" O TRP D 602 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 604 " --> pdb=" O CYS D 607 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS D 607 " --> pdb=" O THR D 604 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 17 through 23 Processing sheet with id=AC1, first strand: chain 'B' and resid 58 through 60 removed outlier: 5.645A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 99 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 125 through 129 removed outlier: 3.757A pdb=" N GLY B 144 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR B 181 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 125 through 129 removed outlier: 3.757A pdb=" N GLY B 144 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR B 181 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 155 through 158 Processing sheet with id=AC5, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.254A pdb=" N VAL C 10 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C 103 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA C 83 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 33 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP C 34 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.254A pdb=" N VAL C 10 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C 103 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA C 83 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 89 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 17 through 23 removed outlier: 3.551A pdb=" N SER C 66 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 114 through 117 removed outlier: 3.598A pdb=" N VAL C 132 " --> pdb=" O PHE C 117 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN C 137 " --> pdb=" O TYR C 172 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR C 172 " --> pdb=" O ASN C 137 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 144 through 149 Processing sheet with id=AD1, first strand: chain 'G' and resid 496 through 498 Processing sheet with id=AD2, first strand: chain 'G' and resid 507 through 509 Processing sheet with id=AD3, first strand: chain 'G' and resid 551 through 555 Processing sheet with id=AD4, first strand: chain 'G' and resid 608 through 609 Processing sheet with id=AD5, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AD6, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.539A pdb=" N MET I 48 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLY I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 125 through 128 removed outlier: 3.605A pdb=" N LYS I 148 " --> pdb=" O SER I 125 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL I 187 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER I 185 " --> pdb=" O CYS I 145 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR I 181 " --> pdb=" O ASP I 149 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 125 through 128 removed outlier: 3.605A pdb=" N LYS I 148 " --> pdb=" O SER I 125 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL I 187 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER I 185 " --> pdb=" O CYS I 145 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR I 181 " --> pdb=" O ASP I 149 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 156 through 159 removed outlier: 4.379A pdb=" N TYR I 199 " --> pdb=" O VAL I 216 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS I 214 " --> pdb=" O CYS I 201 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 9 through 11 removed outlier: 6.900A pdb=" N VAL J 32 " --> pdb=" O TYR J 48 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR J 48 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP J 34 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 9 through 11 Processing sheet with id=AE3, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AE4, first strand: chain 'J' and resid 114 through 117 removed outlier: 3.599A pdb=" N VAL J 132 " --> pdb=" O PHE J 117 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN J 137 " --> pdb=" O TYR J 172 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR J 172 " --> pdb=" O ASN J 137 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 144 through 149 removed outlier: 3.506A pdb=" N GLU J 194 " --> pdb=" O GLN J 146 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS J 148 " --> pdb=" O ALA J 192 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 17 through 21 Processing sheet with id=AE7, first strand: chain 'K' and resid 59 through 60 removed outlier: 3.716A pdb=" N MET K 48 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.615A pdb=" N LYS K 148 " --> pdb=" O SER K 125 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY K 144 " --> pdb=" O LEU K 129 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR K 181 " --> pdb=" O ASP K 149 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.615A pdb=" N LYS K 148 " --> pdb=" O SER K 125 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY K 144 " --> pdb=" O LEU K 129 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR K 181 " --> pdb=" O ASP K 149 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 156 through 159 removed outlier: 3.821A pdb=" N THR K 156 " --> pdb=" O ASN K 204 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.564A pdb=" N VAL L 12 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA L 83 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.564A pdb=" N VAL L 12 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA L 83 " --> pdb=" O LEU L 103 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF5, first strand: chain 'L' and resid 114 through 117 removed outlier: 3.652A pdb=" N VAL L 132 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN L 137 " --> pdb=" O TYR L 172 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR L 172 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 144 through 147 566 hydrogen bonds defined for protein. 1332 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: 7.93 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15134 1.03 - 1.23: 100 1.23 - 1.43: 7144 1.43 - 1.62: 9584 1.62 - 1.82: 130 Bond restraints: 32092 Sorted by residual: bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.70e+00 bond pdb=" C1 NAG Z 1 " pdb=" O5 NAG Z 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.43e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" CB GLN I 65 " pdb=" CG GLN I 65 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 3.96e+00 ... (remaining 32087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 56507 1.48 - 2.96: 949 2.96 - 4.43: 127 4.43 - 5.91: 20 5.91 - 7.39: 8 Bond angle restraints: 57611 Sorted by residual: angle pdb=" N VAL C 46 " pdb=" CA VAL C 46 " pdb=" C VAL C 46 " ideal model delta sigma weight residual 113.53 110.05 3.48 9.80e-01 1.04e+00 1.26e+01 angle pdb=" CA GLN I 65 " pdb=" CB GLN I 65 " pdb=" CG GLN I 65 " ideal model delta sigma weight residual 114.10 120.60 -6.50 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA MET J 80 " pdb=" CB MET J 80 " pdb=" CG MET J 80 " ideal model delta sigma weight residual 114.10 120.46 -6.36 2.00e+00 2.50e-01 1.01e+01 angle pdb=" N PRO D 511 " pdb=" CA PRO D 511 " pdb=" C PRO D 511 " ideal model delta sigma weight residual 112.10 118.77 -6.67 2.60e+00 1.48e-01 6.58e+00 angle pdb=" N THR A 510 " pdb=" CA THR A 510 " pdb=" C THR A 510 " ideal model delta sigma weight residual 109.81 115.45 -5.64 2.21e+00 2.05e-01 6.51e+00 ... (remaining 57606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.92: 14741 24.92 - 49.84: 947 49.84 - 74.76: 183 74.76 - 99.67: 25 99.67 - 124.59: 13 Dihedral angle restraints: 15909 sinusoidal: 8341 harmonic: 7568 Sorted by residual: dihedral pdb=" CB CYS A 459 " pdb=" SG CYS A 459 " pdb=" SG CYS A 486 " pdb=" CB CYS A 486 " ideal model delta sinusoidal sigma weight residual -86.00 -168.17 82.17 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB CYS D 459 " pdb=" SG CYS D 459 " pdb=" SG CYS D 486 " pdb=" CB CYS D 486 " ideal model delta sinusoidal sigma weight residual -86.00 -158.35 72.35 1 1.00e+01 1.00e-02 6.69e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 154.93 -61.93 1 1.00e+01 1.00e-02 5.08e+01 ... (remaining 15906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2325 0.064 - 0.128: 305 0.128 - 0.192: 9 0.192 - 0.256: 3 0.256 - 0.320: 1 Chirality restraints: 2643 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 423 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 540 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C5 BMA Z 3 " pdb=" C4 BMA Z 3 " pdb=" C6 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.51 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2640 not shown) Planarity restraints: 5036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 521 " 0.272 9.50e-02 1.11e+02 9.13e-02 1.03e+01 pdb=" NE ARG A 521 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 521 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 521 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 521 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 521 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 521 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 521 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 521 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 7 " -0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO C 8 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 8 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 8 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 7 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.01e+00 pdb=" N PRO F 8 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 8 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 8 " 0.028 5.00e-02 4.00e+02 ... (remaining 5033 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 546 2.09 - 2.72: 50419 2.72 - 3.35: 81549 3.35 - 3.97: 104013 3.97 - 4.60: 160598 Nonbonded interactions: 397125 Sorted by model distance: nonbonded pdb=" OE1 GLU A 533 " pdb=" H GLU A 533 " model vdw 1.468 2.450 nonbonded pdb=" HH TYR C 2 " pdb=" O ASP C 25 " model vdw 1.565 2.450 nonbonded pdb=" OD1 ASN G 556 " pdb=" H PHE G 560 " model vdw 1.592 2.450 nonbonded pdb=" OD2 ASP E 73 " pdb=" HG1 THR E 76 " model vdw 1.596 2.450 nonbonded pdb="HE21 GLN C 6 " pdb=" O GLY C 99 " model vdw 1.610 2.450 ... (remaining 397120 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 11 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 12 through 22 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ or name OH or name HA or name HB2 or name HB3 or name HD1 or name \ HD2 or name HE1 or name HE2 or name HH )) or resid 33 through 51 or (resid 52 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 53 or (resid 58 and (name N or name CA or name C or name O or name CB or na \ me HA or name HB1 or name HB2 or name HB3)) or resid 59 through 61 or (resid 62 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 63 through 64 or (resid 65 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 66 through 70 or (resid 71 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 72 or \ (resid 79 and (name N or name CA or name C or name O or name CB or name HA or n \ ame HB1 or name HB2 or name HB3)) or resid 80 through 81 or (resid 82 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 83 \ through 94 or (resid 95 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 96 through 102 or (resid 103 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 104 through 1 \ 12 or (resid 113 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 114 through 134 or (resid 135 through 137 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 138 thr \ ough 220 or (resid 221 and (name N or name CA or name C or name O or name CB or \ name SG or name H or name HA or name HB2 or name HB3)))) selection = (chain 'E' and ((resid 11 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 12 through 18 or (resid 19 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 20 through 22 or (resid \ 32 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2 or name CE1 or name CE2 or name CZ or name OH or name HA or name HB \ 2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HH )) or r \ esid 33 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 47 through 51 or (resid 52 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 53 or ( \ resid 58 and (name N or name CA or name C or name O or name CB or name HA or nam \ e HB1 or name HB2 or name HB3)) or resid 59 through 61 or (resid 62 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 63 th \ rough 64 or (resid 65 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 66 through 70 or (resid 71 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 72 or (resid 79 a \ nd (name N or name CA or name C or name O or name CB or name HA or name HB1 or n \ ame HB2 or name HB3)) or resid 80 through 81 or (resid 82 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 83 through 94 o \ r (resid 95 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 96 through 102 or (resid 103 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 104 through 112 or (resid \ 113 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 114 through 134 or (resid 135 through 137 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 138 through 220 or \ (resid 221 and (name N or name CA or name C or name O or name CB or name SG or n \ ame H or name HA or name HB2 or name HB3)))) selection = (chain 'I' and ((resid 11 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 12 or (resid 13 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 14 through 18 or (resid 19 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 20 through 22 or (resid 32 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name O \ H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name \ HE2 or name HH )) or resid 33 through 45 or (resid 46 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 47 through 51 or ( \ resid 52 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 53 or (resid 58 and (name N or name CA or name C or name O or na \ me CB or name HA or name HB1 or name HB2 or name HB3)) or resid 59 through 61 or \ (resid 62 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 63 through 64 or (resid 65 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 66 through 70 or (resid 71 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 72 or (resid 79 and (name N or name CA or name C or name O or name CB or n \ ame HA or name HB1 or name HB2 or name HB3)) or resid 80 through 81 or (resid 82 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 83 through 94 or (resid 95 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 96 through 112 or (resid 113 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 11 \ 4 through 133 or (resid 134 through 137 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 138 through 221)) selection = (chain 'K' and (resid 11 through 133 or (resid 134 through 137 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 138 throug \ h 220 or (resid 221 and (name N or name CA or name C or name O or name CB or nam \ e SG or name H or name HA or name HB2 or name HB3)))) } ncs_group { reference = (chain 'C' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 6 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 21 through 29 or (resid 3 \ 0 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 31 through 36 or (resid 37 through 38 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 39 through 45 or (resid 46 \ through 47 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 48 through 51 or (resid 52 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 53 through 54 or resid 58 o \ r (resid 59 through 60 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 61 through 63 or (resid 64 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 65 or (resid 66 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 67 through 71 or (resid 72 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 73 through 74 or (resid 75 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 76 th \ rough 77 or (resid 78 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 79 through 80 or (resid 81 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 82 through 90 or \ (resid 91 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or (resid 94 and (name N or name CA or name C or name O or name CB or na \ me HA or name HB1 or name HB2 or name HB3)) or resid 95 or (resid 96 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 97 t \ hrough 101 or (resid 102 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 103 through 180 or (resid 181 through 182 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 183 through 211 or (resid 212 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or (resid 213 and (name N or name CA or name C or n \ ame CB or name SG or name H or name HA or name HB2 or name HB3)))) selection = (chain 'F' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 6 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 21 through 25 or (resid 2 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 27 through 28 or (resid 29 through 30 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 31 through 36 or (resid 37 \ through 38 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 39 through 45 or (resid 46 through 47 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 48 through 51 or \ (resid 52 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 53 through 54 or resid 58 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 61 th \ rough 63 or (resid 64 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 65 or (resid 66 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 67 through 71 or (resid 72 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 73 through 74 or (resid 75 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 76 through 77 or (resid 78 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 79 thr \ ough 80 or (resid 81 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 82 through 90 or (resid 91 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or (resid 94 and (name N or \ name CA or name C or name O or name CB or name HA or name HB1 or name HB2 or na \ me HB3)) or resid 95 or (resid 96 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 97 through 101 or (resid 102 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 103 \ through 165 or (resid 166 through 168 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 169 through 180 or (resid 181 thro \ ugh 182 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 183 through 211 or (resid 212 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or (resid 213 and (name N or name CA \ or name C or name CB or name SG or name H or name HA or name HB2 or name HB3)))) \ selection = (chain 'J' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 6 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 21 through 25 or (resid 2 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 27 through 28 or (resid 29 through 30 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 31 through 36 or (resid 37 \ through 38 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 39 through 45 or (resid 46 through 47 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 48 through 54 or \ resid 58 through 59 or (resid 60 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 61 through 63 or (resid 64 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 65 or \ (resid 66 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 67 through 71 or (resid 72 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 73 through 74 or (resid 75 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 76 through 77 or (resid 78 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 79 through 80 or (resid 81 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 82 thr \ ough 90 or (resid 91 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or (resid 94 and (name N or name CA or name C or name O or na \ me CB or name HA or name HB1 or name HB2 or name HB3)) or resid 95 or (resid 96 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 97 through 101 or (resid 102 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 103 through 165 or (resid 166 through \ 168 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 169 through 180 or (resid 181 through 182 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 183 through 211 or \ (resid 212 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or (resid 213 and (name N or name CA or name C or name CB or name SG or \ name H or name HA or name HB2 or name HB3)))) selection = (chain 'L' and (resid 5 through 28 or (resid 29 through 30 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 31 through 213 \ )) } ncs_group { reference = (chain 'D' and ((resid 417 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 418 through 424 or (resid 425 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 426 through 434 or \ (resid 435 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 436 through 461 or (resid 485 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 486 through 499 or (resid \ 500 through 502 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 503 through 506 or (resid 507 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 508 through 515 or \ (resid 516 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 519 or (resid 528 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 532 through 569 or (resid 593 and (na \ me N or name CA or name C or name O or name CB or name HA )) or resid 594 throug \ h 605 or (resid 606 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 607 through 608 or (resid 609 through 610 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 611 \ through 624 or (resid 625 through 627 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or (resid 639 and (name N or name CA or name \ C or name O or name CB or name HA )) or resid 640 through 646)) selection = (chain 'G' and ((resid 417 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 418 through 419 or (resid 420 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 421 through 431 or \ (resid 432 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 433 through 436 or (resid 437 through 438 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 439 through 4 \ 49 or (resid 450 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 451 through 455 or (resid 456 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 457 through 487 or \ (resid 488 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 489 through 492 or (resid 493 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 494 through 500 or (resid \ 501 through 502 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 503 through 516 or resid 528 or resid 534 or resid 541 o \ r (resid 542 and (name N or name CA or name C or name O or name CB or name OG1 o \ r name CG2 or name HA or name HB or name HG1 or name HG21 or name HG22 or name H \ G23)) or resid 543 through 547 or (resid 548 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 549 or (resid 550 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 551 \ through 561 or (resid 562 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 563 through 569 or resid 593 through 603 or (r \ esid 604 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 605 through 626 or (resid 627 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 639 through 645 or (resid 6 \ 46 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ )) } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'N' } 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 group one per residue 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: 1.120 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: 0.240 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.140 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17002 Z= 0.142 Angle : 0.556 10.380 23302 Z= 0.267 Chirality : 0.044 0.320 2643 Planarity : 0.004 0.120 2975 Dihedral : 16.859 124.593 5939 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.17 % Allowed : 22.33 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.19), residues: 2180 helix: -1.16 (0.57), residues: 90 sheet: 0.64 (0.19), residues: 797 loop : -0.84 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A 521 TYR 0.013 0.001 TYR I 80 PHE 0.009 0.001 PHE L 138 TRP 0.006 0.001 TRP E 36 HIS 0.003 0.001 HIS E 169 Details of bonding type rmsd covalent geometry : bond 0.00322 (16952) covalent geometry : angle 0.54463 (23192) SS BOND : bond 0.00235 ( 40) SS BOND : angle 0.51534 ( 80) hydrogen bonds : bond 0.27196 ( 505) hydrogen bonds : angle 9.61585 ( 1332) link_BETA1-4 : bond 0.00998 ( 5) link_BETA1-4 : angle 3.78055 ( 15) link_NAG-ASN : bond 0.00645 ( 5) link_NAG-ASN : angle 2.37339 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue VAL 574 is missing expected H atoms. Skipping. Residue THR 578 is missing expected H atoms. Skipping. Residue LEU 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS F 213 " (corrupted residue). Skipping it. Residue THR 416 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue LEU 438 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue THR 604 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue MET 631 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue VAL 636 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS C 213 " (corrupted residue). Skipping it. Residue SER 419 is missing expected H atoms. Skipping. Residue THR 425 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue SER 500 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue THR 534 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 593 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue VAL 609 is missing expected H atoms. Skipping. Residue THR 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP I 222 " (corrupted residue). Skipping it. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS J 213 " (corrupted residue). Skipping it. Residue VAL 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS L 213 " (corrupted residue). Skipping it. Evaluate side-chains 184 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 181 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 48 MET cc_start: 0.7406 (ppp) cc_final: 0.6842 (ppp) outliers start: 3 outliers final: 2 residues processed: 184 average time/residue: 0.2658 time to fit residues: 74.3171 Evaluate side-chains 175 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain D residue 423 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.0970 chunk 212 optimal weight: 0.5980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN J 123 GLN J 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.171254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117451 restraints weight = 73754.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120111 restraints weight = 46371.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120746 restraints weight = 32973.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120799 restraints weight = 29542.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.122726 restraints weight = 28294.084| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17002 Z= 0.171 Angle : 0.615 7.226 23302 Z= 0.315 Chirality : 0.045 0.267 2643 Planarity : 0.004 0.049 2975 Dihedral : 11.010 116.885 2587 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.94 % Favored : 92.02 % Rotamer: Outliers : 1.33 % Allowed : 22.22 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.18), residues: 2180 helix: -1.03 (0.58), residues: 90 sheet: 0.77 (0.19), residues: 823 loop : -0.95 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 521 TYR 0.018 0.001 TYR I 80 PHE 0.016 0.001 PHE L 208 TRP 0.010 0.001 TRP B 159 HIS 0.004 0.001 HIS E 169 Details of bonding type rmsd covalent geometry : bond 0.00398 (16952) covalent geometry : angle 0.60872 (23192) SS BOND : bond 0.00382 ( 40) SS BOND : angle 0.73679 ( 80) hydrogen bonds : bond 0.05457 ( 505) hydrogen bonds : angle 7.15500 ( 1332) link_BETA1-4 : bond 0.00580 ( 5) link_BETA1-4 : angle 2.41601 ( 15) link_NAG-ASN : bond 0.00549 ( 5) link_NAG-ASN : angle 2.48347 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue VAL 574 is missing expected H atoms. Skipping. Residue THR 578 is missing expected H atoms. Skipping. Residue LEU 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS F 213 " (corrupted residue). Skipping it. Residue THR 416 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue LEU 438 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue THR 604 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue MET 631 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue VAL 636 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS C 213 " (corrupted residue). Skipping it. Residue SER 419 is missing expected H atoms. Skipping. Residue THR 425 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue SER 500 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue THR 534 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 593 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue VAL 609 is missing expected H atoms. Skipping. Residue THR 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP I 222 " (corrupted residue). Skipping it. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS J 213 " (corrupted residue). Skipping it. Residue VAL 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS L 213 " (corrupted residue). Skipping it. Evaluate side-chains 207 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 91 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.6996 (p0) REVERT: J 123 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: K 48 MET cc_start: 0.7417 (ppp) cc_final: 0.6880 (ppp) outliers start: 23 outliers final: 15 residues processed: 201 average time/residue: 0.2474 time to fit residues: 77.0422 Evaluate side-chains 189 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain D residue 423 ASN Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain K residue 184 SER Chi-restraints excluded: chain L residue 84 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 69 optimal weight: 0.0050 chunk 127 optimal weight: 9.9990 chunk 44 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.170816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115680 restraints weight = 74030.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118921 restraints weight = 45697.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.120107 restraints weight = 34258.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120962 restraints weight = 28405.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.121387 restraints weight = 28029.067| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17002 Z= 0.165 Angle : 0.599 7.972 23302 Z= 0.302 Chirality : 0.045 0.262 2643 Planarity : 0.004 0.046 2975 Dihedral : 10.554 114.719 2587 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.12 % Favored : 91.83 % Rotamer: Outliers : 2.15 % Allowed : 21.93 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.18), residues: 2180 helix: -1.23 (0.58), residues: 84 sheet: 0.66 (0.18), residues: 824 loop : -0.97 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 521 TYR 0.015 0.001 TYR F 48 PHE 0.014 0.001 PHE L 208 TRP 0.010 0.001 TRP B 159 HIS 0.004 0.001 HIS E 169 Details of bonding type rmsd covalent geometry : bond 0.00389 (16952) covalent geometry : angle 0.59346 (23192) SS BOND : bond 0.00351 ( 40) SS BOND : angle 0.66604 ( 80) hydrogen bonds : bond 0.04418 ( 505) hydrogen bonds : angle 6.46972 ( 1332) link_BETA1-4 : bond 0.00537 ( 5) link_BETA1-4 : angle 2.36280 ( 15) link_NAG-ASN : bond 0.00538 ( 5) link_NAG-ASN : angle 2.39015 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue VAL 574 is missing expected H atoms. Skipping. Residue THR 578 is missing expected H atoms. Skipping. Residue LEU 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS F 213 " (corrupted residue). Skipping it. Residue THR 416 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue LEU 438 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue THR 604 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue MET 631 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue VAL 636 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS C 213 " (corrupted residue). Skipping it. Residue SER 419 is missing expected H atoms. Skipping. Residue THR 425 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue SER 500 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue THR 534 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 593 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue VAL 609 is missing expected H atoms. Skipping. Residue THR 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP I 222 " (corrupted residue). Skipping it. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS J 213 " (corrupted residue). Skipping it. Residue VAL 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS L 213 " (corrupted residue). Skipping it. Evaluate side-chains 217 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.6659 (tpp) cc_final: 0.6360 (tpt) REVERT: F 159 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: I 65 GLN cc_start: 0.8404 (pp30) cc_final: 0.7918 (pp30) REVERT: J 91 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.6956 (p0) REVERT: K 48 MET cc_start: 0.7593 (ppp) cc_final: 0.7016 (ppp) REVERT: L 107 ARG cc_start: 0.7471 (tpt-90) cc_final: 0.7210 (tpt-90) outliers start: 37 outliers final: 33 residues processed: 207 average time/residue: 0.2457 time to fit residues: 79.6570 Evaluate side-chains 202 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 GLN Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 193 CYS Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain D residue 423 ASN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain G residue 552 CYS Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 184 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 210 optimal weight: 0.8980 chunk 110 optimal weight: 0.4980 chunk 165 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.169392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.113311 restraints weight = 74001.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117404 restraints weight = 43885.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118916 restraints weight = 32199.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.119816 restraints weight = 26029.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.120247 restraints weight = 23809.119| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17002 Z= 0.129 Angle : 0.575 9.038 23302 Z= 0.286 Chirality : 0.044 0.266 2643 Planarity : 0.004 0.046 2975 Dihedral : 10.088 113.583 2585 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.48 % Favored : 92.48 % Rotamer: Outliers : 2.32 % Allowed : 21.98 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.18), residues: 2180 helix: -1.11 (0.60), residues: 78 sheet: 0.64 (0.18), residues: 823 loop : -0.91 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 521 TYR 0.011 0.001 TYR F 48 PHE 0.027 0.001 PHE A 509 TRP 0.011 0.001 TRP D 487 HIS 0.003 0.001 HIS E 169 Details of bonding type rmsd covalent geometry : bond 0.00307 (16952) covalent geometry : angle 0.56943 (23192) SS BOND : bond 0.00315 ( 40) SS BOND : angle 0.60112 ( 80) hydrogen bonds : bond 0.03613 ( 505) hydrogen bonds : angle 6.08939 ( 1332) link_BETA1-4 : bond 0.00513 ( 5) link_BETA1-4 : angle 2.32524 ( 15) link_NAG-ASN : bond 0.00529 ( 5) link_NAG-ASN : angle 2.41409 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue VAL 574 is missing expected H atoms. Skipping. Residue THR 578 is missing expected H atoms. Skipping. Residue LEU 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS F 213 " (corrupted residue). Skipping it. Residue THR 416 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue LEU 438 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue THR 604 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue MET 631 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue VAL 636 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS C 213 " (corrupted residue). Skipping it. Residue SER 419 is missing expected H atoms. Skipping. Residue THR 425 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue SER 500 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue THR 534 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 593 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue VAL 609 is missing expected H atoms. Skipping. Residue THR 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP I 222 " (corrupted residue). Skipping it. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS J 213 " (corrupted residue). Skipping it. Residue VAL 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS L 213 " (corrupted residue). Skipping it. Evaluate side-chains 220 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.7283 (tpp) cc_final: 0.6973 (tpp) REVERT: F 159 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7898 (mt0) REVERT: B 31 ASN cc_start: 0.7301 (t0) cc_final: 0.7100 (t0) REVERT: I 65 GLN cc_start: 0.8360 (pp30) cc_final: 0.7874 (pp30) REVERT: J 91 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7200 (p0) REVERT: K 48 MET cc_start: 0.7317 (ppp) cc_final: 0.6823 (ppp) REVERT: L 107 ARG cc_start: 0.7309 (tpt-90) cc_final: 0.6975 (tpt170) outliers start: 40 outliers final: 33 residues processed: 211 average time/residue: 0.2505 time to fit residues: 82.7226 Evaluate side-chains 206 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 GLN Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 193 CYS Chi-restraints excluded: chain D residue 423 ASN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain G residue 552 CYS Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 122 GLU Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 184 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 86 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 210 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.168237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111863 restraints weight = 74302.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115775 restraints weight = 44558.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117741 restraints weight = 32176.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118873 restraints weight = 26350.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119643 restraints weight = 23359.048| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17002 Z= 0.170 Angle : 0.595 9.865 23302 Z= 0.296 Chirality : 0.044 0.263 2643 Planarity : 0.004 0.045 2975 Dihedral : 9.838 113.915 2585 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.21 % Favored : 91.74 % Rotamer: Outliers : 2.90 % Allowed : 21.69 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.18), residues: 2180 helix: -1.07 (0.61), residues: 78 sheet: 0.58 (0.18), residues: 821 loop : -0.95 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 38 TYR 0.017 0.001 TYR F 48 PHE 0.022 0.001 PHE A 509 TRP 0.018 0.001 TRP G 554 HIS 0.004 0.001 HIS E 169 Details of bonding type rmsd covalent geometry : bond 0.00404 (16952) covalent geometry : angle 0.58860 (23192) SS BOND : bond 0.00329 ( 40) SS BOND : angle 0.66635 ( 80) hydrogen bonds : bond 0.03594 ( 505) hydrogen bonds : angle 5.97101 ( 1332) link_BETA1-4 : bond 0.00491 ( 5) link_BETA1-4 : angle 2.37559 ( 15) link_NAG-ASN : bond 0.00540 ( 5) link_NAG-ASN : angle 2.37430 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue VAL 574 is missing expected H atoms. Skipping. Residue THR 578 is missing expected H atoms. Skipping. Residue LEU 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS F 213 " (corrupted residue). Skipping it. Residue THR 416 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue LEU 438 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue THR 604 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue MET 631 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue VAL 636 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS C 213 " (corrupted residue). Skipping it. Residue SER 419 is missing expected H atoms. Skipping. Residue THR 425 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue SER 500 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue THR 534 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 593 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue VAL 609 is missing expected H atoms. Skipping. Residue THR 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP I 222 " (corrupted residue). Skipping it. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS J 213 " (corrupted residue). Skipping it. Residue VAL 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS L 213 " (corrupted residue). Skipping it. Evaluate side-chains 223 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.7622 (mp10) cc_final: 0.6467 (tp40) REVERT: A 631 MET cc_start: 0.7277 (tpp) cc_final: 0.7042 (tpp) REVERT: F 159 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7913 (mt0) REVERT: D 555 MET cc_start: 0.7874 (tpp) cc_final: 0.7348 (tpt) REVERT: B 31 ASN cc_start: 0.7276 (t0) cc_final: 0.6995 (t0) REVERT: I 10 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8088 (pp20) REVERT: I 59 MET cc_start: 0.6275 (mtp) cc_final: 0.6023 (mtp) REVERT: I 65 GLN cc_start: 0.8240 (pp30) cc_final: 0.7832 (pp30) REVERT: J 91 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.7329 (p0) REVERT: K 48 MET cc_start: 0.7364 (ppp) cc_final: 0.6941 (ppp) REVERT: L 107 ARG cc_start: 0.7437 (tpt-90) cc_final: 0.7044 (tpt170) outliers start: 50 outliers final: 40 residues processed: 214 average time/residue: 0.2498 time to fit residues: 84.7241 Evaluate side-chains 212 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 GLN Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 193 CYS Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain D residue 423 ASN Chi-restraints excluded: chain D residue 428 ASN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain G residue 552 CYS Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 184 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 148 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 75 optimal weight: 20.0000 chunk 195 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.169566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.113503 restraints weight = 74097.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.117614 restraints weight = 45180.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119300 restraints weight = 33404.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120139 restraints weight = 26856.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120604 restraints weight = 25134.241| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17002 Z= 0.131 Angle : 0.576 10.893 23302 Z= 0.284 Chirality : 0.044 0.261 2643 Planarity : 0.004 0.043 2975 Dihedral : 9.468 114.102 2585 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.06 % Favored : 92.89 % Rotamer: Outliers : 2.26 % Allowed : 22.33 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.18), residues: 2180 helix: -1.03 (0.61), residues: 78 sheet: 0.58 (0.18), residues: 821 loop : -0.89 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 98 TYR 0.012 0.001 TYR I 80 PHE 0.017 0.001 PHE A 509 TRP 0.013 0.001 TRP D 487 HIS 0.003 0.001 HIS E 169 Details of bonding type rmsd covalent geometry : bond 0.00316 (16952) covalent geometry : angle 0.56937 (23192) SS BOND : bond 0.00313 ( 40) SS BOND : angle 0.60553 ( 80) hydrogen bonds : bond 0.03234 ( 505) hydrogen bonds : angle 5.76939 ( 1332) link_BETA1-4 : bond 0.00472 ( 5) link_BETA1-4 : angle 2.48125 ( 15) link_NAG-ASN : bond 0.00519 ( 5) link_NAG-ASN : angle 2.37098 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue VAL 574 is missing expected H atoms. Skipping. Residue THR 578 is missing expected H atoms. Skipping. Residue LEU 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS F 213 " (corrupted residue). Skipping it. Residue THR 416 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue LEU 438 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue THR 604 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue MET 631 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue VAL 636 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS C 213 " (corrupted residue). Skipping it. Residue SER 419 is missing expected H atoms. Skipping. Residue THR 425 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue SER 500 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue THR 534 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 593 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue VAL 609 is missing expected H atoms. Skipping. Residue THR 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP I 222 " (corrupted residue). Skipping it. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS J 213 " (corrupted residue). Skipping it. Residue VAL 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS L 213 " (corrupted residue). Skipping it. Evaluate side-chains 217 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.7688 (mp10) cc_final: 0.6495 (tp40) REVERT: A 631 MET cc_start: 0.7289 (tpp) cc_final: 0.7059 (tpp) REVERT: F 91 ASP cc_start: 0.7571 (t0) cc_final: 0.7334 (t0) REVERT: F 159 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: B 31 ASN cc_start: 0.7225 (t0) cc_final: 0.6893 (t0) REVERT: I 59 MET cc_start: 0.6688 (mtp) cc_final: 0.6484 (mtp) REVERT: I 65 GLN cc_start: 0.8250 (pp30) cc_final: 0.7820 (pp30) REVERT: J 91 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7238 (p0) REVERT: K 48 MET cc_start: 0.7391 (ppp) cc_final: 0.6987 (ppp) REVERT: L 107 ARG cc_start: 0.7358 (tpt-90) cc_final: 0.7083 (tpt170) outliers start: 39 outliers final: 37 residues processed: 208 average time/residue: 0.2552 time to fit residues: 83.5454 Evaluate side-chains 207 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 159 GLN Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 193 CYS Chi-restraints excluded: chain D residue 423 ASN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain G residue 552 CYS Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 184 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 128 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 82 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 211 optimal weight: 0.0040 chunk 219 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.170884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131441 restraints weight = 74208.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.133685 restraints weight = 86140.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.134364 restraints weight = 70232.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.135866 restraints weight = 38511.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.136348 restraints weight = 31816.313| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17002 Z= 0.098 Angle : 0.561 10.138 23302 Z= 0.274 Chirality : 0.044 0.261 2643 Planarity : 0.004 0.042 2975 Dihedral : 8.946 114.143 2585 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.61 % Favored : 93.35 % Rotamer: Outliers : 2.15 % Allowed : 22.74 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.18), residues: 2180 helix: -1.00 (0.61), residues: 78 sheet: 0.66 (0.19), residues: 821 loop : -0.82 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 98 TYR 0.011 0.001 TYR I 80 PHE 0.016 0.001 PHE A 509 TRP 0.014 0.001 TRP D 487 HIS 0.002 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00234 (16952) covalent geometry : angle 0.55316 (23192) SS BOND : bond 0.00362 ( 40) SS BOND : angle 0.79351 ( 80) hydrogen bonds : bond 0.02925 ( 505) hydrogen bonds : angle 5.52689 ( 1332) link_BETA1-4 : bond 0.00420 ( 5) link_BETA1-4 : angle 2.63875 ( 15) link_NAG-ASN : bond 0.00518 ( 5) link_NAG-ASN : angle 2.44405 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue VAL 574 is missing expected H atoms. Skipping. Residue THR 578 is missing expected H atoms. Skipping. Residue LEU 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS F 213 " (corrupted residue). Skipping it. Residue THR 416 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue LEU 438 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue THR 604 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue MET 631 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue VAL 636 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS C 213 " (corrupted residue). Skipping it. Residue SER 419 is missing expected H atoms. Skipping. Residue THR 425 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue SER 500 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue THR 534 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 593 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue VAL 609 is missing expected H atoms. Skipping. Residue THR 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP I 222 " (corrupted residue). Skipping it. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS J 213 " (corrupted residue). Skipping it. Residue VAL 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS L 213 " (corrupted residue). Skipping it. Evaluate side-chains 222 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.7092 (mp10) cc_final: 0.6186 (tp40) REVERT: F 91 ASP cc_start: 0.7537 (t0) cc_final: 0.7248 (t0) REVERT: F 159 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7820 (mt0) REVERT: B 31 ASN cc_start: 0.7044 (t0) cc_final: 0.6628 (t0) REVERT: I 65 GLN cc_start: 0.8311 (pp30) cc_final: 0.7863 (pp30) REVERT: J 91 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.7412 (p0) REVERT: K 48 MET cc_start: 0.6330 (ppp) cc_final: 0.6029 (ppp) outliers start: 37 outliers final: 32 residues processed: 215 average time/residue: 0.2564 time to fit residues: 86.7484 Evaluate side-chains 209 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 159 GLN Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 193 CYS Chi-restraints excluded: chain D residue 423 ASN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain G residue 552 CYS Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 184 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 142 optimal weight: 0.2980 chunk 181 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.168897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.112213 restraints weight = 74219.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.116675 restraints weight = 45083.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118372 restraints weight = 31384.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119591 restraints weight = 26252.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.120354 restraints weight = 23113.258| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17002 Z= 0.155 Angle : 0.576 7.999 23302 Z= 0.285 Chirality : 0.044 0.258 2643 Planarity : 0.004 0.042 2975 Dihedral : 8.755 113.845 2585 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.26 % Allowed : 23.20 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.18), residues: 2180 helix: -1.01 (0.61), residues: 78 sheet: 0.62 (0.19), residues: 821 loop : -0.88 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 98 TYR 0.021 0.001 TYR E 106 PHE 0.014 0.001 PHE A 509 TRP 0.014 0.001 TRP D 487 HIS 0.004 0.001 HIS E 169 Details of bonding type rmsd covalent geometry : bond 0.00373 (16952) covalent geometry : angle 0.56959 (23192) SS BOND : bond 0.00305 ( 40) SS BOND : angle 0.65326 ( 80) hydrogen bonds : bond 0.03137 ( 505) hydrogen bonds : angle 5.54314 ( 1332) link_BETA1-4 : bond 0.00400 ( 5) link_BETA1-4 : angle 2.23202 ( 15) link_NAG-ASN : bond 0.00529 ( 5) link_NAG-ASN : angle 2.43430 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue VAL 574 is missing expected H atoms. Skipping. Residue THR 578 is missing expected H atoms. Skipping. Residue LEU 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS F 213 " (corrupted residue). Skipping it. Residue THR 416 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue LEU 438 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue THR 604 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue MET 631 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue VAL 636 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS C 213 " (corrupted residue). Skipping it. Residue SER 419 is missing expected H atoms. Skipping. Residue THR 425 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue SER 500 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue THR 534 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 593 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue VAL 609 is missing expected H atoms. Skipping. Residue THR 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP I 222 " (corrupted residue). Skipping it. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS J 213 " (corrupted residue). Skipping it. Residue VAL 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS L 213 " (corrupted residue). Skipping it. Evaluate side-chains 212 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.7593 (mp10) cc_final: 0.6436 (tp40) REVERT: A 631 MET cc_start: 0.7294 (tpp) cc_final: 0.6821 (tpt) REVERT: F 91 ASP cc_start: 0.7575 (t0) cc_final: 0.7307 (t0) REVERT: F 159 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7867 (mt0) REVERT: D 555 MET cc_start: 0.7702 (tpp) cc_final: 0.7205 (tpt) REVERT: B 31 ASN cc_start: 0.7342 (t0) cc_final: 0.6953 (t0) REVERT: I 65 GLN cc_start: 0.8320 (pp30) cc_final: 0.7832 (pp30) REVERT: J 91 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7239 (p0) REVERT: K 48 MET cc_start: 0.7328 (ppp) cc_final: 0.6950 (ppp) outliers start: 39 outliers final: 35 residues processed: 205 average time/residue: 0.2461 time to fit residues: 79.9763 Evaluate side-chains 209 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 159 GLN Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 193 CYS Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain G residue 552 CYS Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 184 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 200 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 145 optimal weight: 0.0470 chunk 207 optimal weight: 8.9990 chunk 31 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.170249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.115910 restraints weight = 74133.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118911 restraints weight = 46623.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119363 restraints weight = 32022.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119448 restraints weight = 31195.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119874 restraints weight = 29524.649| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17002 Z= 0.112 Angle : 0.569 9.913 23302 Z= 0.282 Chirality : 0.044 0.257 2643 Planarity : 0.004 0.041 2975 Dihedral : 8.647 114.395 2583 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.88 % Favored : 93.07 % Rotamer: Outliers : 2.15 % Allowed : 23.26 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.18), residues: 2180 helix: -0.98 (0.61), residues: 78 sheet: 0.65 (0.19), residues: 821 loop : -0.84 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 98 TYR 0.022 0.001 TYR E 106 PHE 0.014 0.001 PHE A 509 TRP 0.015 0.001 TRP D 487 HIS 0.003 0.001 HIS E 169 Details of bonding type rmsd covalent geometry : bond 0.00270 (16952) covalent geometry : angle 0.56294 (23192) SS BOND : bond 0.00388 ( 40) SS BOND : angle 0.83538 ( 80) hydrogen bonds : bond 0.02909 ( 505) hydrogen bonds : angle 5.42754 ( 1332) link_BETA1-4 : bond 0.00393 ( 5) link_BETA1-4 : angle 2.00282 ( 15) link_NAG-ASN : bond 0.00518 ( 5) link_NAG-ASN : angle 2.43660 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue VAL 574 is missing expected H atoms. Skipping. Residue THR 578 is missing expected H atoms. Skipping. Residue LEU 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS F 213 " (corrupted residue). Skipping it. Residue THR 416 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue LEU 438 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue THR 604 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue MET 631 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue VAL 636 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS C 213 " (corrupted residue). Skipping it. Residue SER 419 is missing expected H atoms. Skipping. Residue THR 425 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue SER 500 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue THR 534 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 593 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue VAL 609 is missing expected H atoms. Skipping. Residue THR 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP I 222 " (corrupted residue). Skipping it. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS J 213 " (corrupted residue). Skipping it. Residue VAL 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS L 213 " (corrupted residue). Skipping it. Evaluate side-chains 214 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.7723 (mp10) cc_final: 0.6477 (tp40) REVERT: F 91 ASP cc_start: 0.7540 (t0) cc_final: 0.7282 (t0) REVERT: F 159 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: D 555 MET cc_start: 0.7826 (tpp) cc_final: 0.7425 (tpt) REVERT: B 31 ASN cc_start: 0.7208 (t0) cc_final: 0.6816 (t0) REVERT: I 65 GLN cc_start: 0.8354 (pp30) cc_final: 0.7942 (pp30) REVERT: J 91 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.7279 (p0) REVERT: K 48 MET cc_start: 0.7196 (ppp) cc_final: 0.6766 (ppp) outliers start: 37 outliers final: 35 residues processed: 207 average time/residue: 0.2547 time to fit residues: 82.9408 Evaluate side-chains 211 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 221 CYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 159 GLN Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 193 CYS Chi-restraints excluded: chain D residue 428 ASN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain G residue 552 CYS Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain J residue 87 CYS Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 184 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 79 optimal weight: 0.0570 chunk 16 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 62 optimal weight: 0.0980 chunk 123 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 42 optimal weight: 0.1980 chunk 188 optimal weight: 8.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.171163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.130719 restraints weight = 74133.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.129376 restraints weight = 97478.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131963 restraints weight = 73653.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132848 restraints weight = 42849.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.134459 restraints weight = 36784.863| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 17002 Z= 0.097 Angle : 0.557 8.744 23302 Z= 0.274 Chirality : 0.044 0.257 2643 Planarity : 0.004 0.041 2975 Dihedral : 8.473 114.905 2583 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.79 % Favored : 93.17 % Rotamer: Outliers : 1.91 % Allowed : 23.49 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.18), residues: 2180 helix: -0.97 (0.60), residues: 78 sheet: 0.70 (0.19), residues: 821 loop : -0.79 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 98 TYR 0.020 0.001 TYR E 106 PHE 0.014 0.001 PHE A 509 TRP 0.017 0.001 TRP D 487 HIS 0.002 0.001 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00237 (16952) covalent geometry : angle 0.55187 (23192) SS BOND : bond 0.00358 ( 40) SS BOND : angle 0.72143 ( 80) hydrogen bonds : bond 0.02758 ( 505) hydrogen bonds : angle 5.27985 ( 1332) link_BETA1-4 : bond 0.00403 ( 5) link_BETA1-4 : angle 1.87057 ( 15) link_NAG-ASN : bond 0.00524 ( 5) link_NAG-ASN : angle 2.36822 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue SER 480 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue VAL 574 is missing expected H atoms. Skipping. Residue THR 578 is missing expected H atoms. Skipping. Residue LEU 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS F 213 " (corrupted residue). Skipping it. Residue THR 416 is missing expected H atoms. Skipping. Residue SER 419 is missing expected H atoms. Skipping. Residue SER 432 is missing expected H atoms. Skipping. Residue LEU 438 is missing expected H atoms. Skipping. Residue SER 450 is missing expected H atoms. Skipping. Residue MET 456 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue LYS 562 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue THR 604 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue MET 631 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue VAL 636 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS C 213 " (corrupted residue). Skipping it. Residue SER 419 is missing expected H atoms. Skipping. Residue THR 425 is missing expected H atoms. Skipping. Residue THR 435 is missing expected H atoms. Skipping. Residue TYR 485 is missing expected H atoms. Skipping. Residue THR 496 is missing expected H atoms. Skipping. Residue SER 500 is missing expected H atoms. Skipping. Residue TYR 507 is missing expected H atoms. Skipping. Residue VAL 516 is missing expected H atoms. Skipping. Residue THR 534 is missing expected H atoms. Skipping. Residue ILE 538 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue THR 593 is missing expected H atoms. Skipping. Residue TYR 594 is missing expected H atoms. Skipping. Residue THR 595 is missing expected H atoms. Skipping. Residue LYS 596 is missing expected H atoms. Skipping. Residue LEU 603 is missing expected H atoms. Skipping. Residue VAL 609 is missing expected H atoms. Skipping. Residue THR 625 is missing expected H atoms. Skipping. Residue ILE 626 is missing expected H atoms. Skipping. Residue LEU 640 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "ASP I 222 " (corrupted residue). Skipping it. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS J 213 " (corrupted residue). Skipping it. Residue VAL 11 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 19 is missing expected H atoms. Skipping. Residue ILE 52 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue SER 135 is missing expected H atoms. Skipping. Residue SER 137 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue SER 75 is missing expected H atoms. Skipping. Residue VAL 96 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue SER 167 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "CYS L 213 " (corrupted residue). Skipping it. Evaluate side-chains 213 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 GLN cc_start: 0.7036 (mp10) cc_final: 0.6049 (tp40) REVERT: F 91 ASP cc_start: 0.7506 (t0) cc_final: 0.7234 (t0) REVERT: F 159 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: B 31 ASN cc_start: 0.7103 (t0) cc_final: 0.6700 (t0) REVERT: I 65 GLN cc_start: 0.8306 (pp30) cc_final: 0.7881 (pp30) REVERT: J 91 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7407 (p0) REVERT: K 48 MET cc_start: 0.6277 (ppp) cc_final: 0.5937 (ppp) outliers start: 33 outliers final: 30 residues processed: 207 average time/residue: 0.2607 time to fit residues: 84.2219 Evaluate side-chains 207 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 458 HIS Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 159 GLN Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain G residue 552 CYS Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 184 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain L residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 196 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 145 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.169836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.128786 restraints weight = 74294.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127072 restraints weight = 93144.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129393 restraints weight = 74025.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130682 restraints weight = 39578.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132142 restraints weight = 33500.750| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17002 Z= 0.139 Angle : 0.576 12.567 23302 Z= 0.284 Chirality : 0.044 0.257 2643 Planarity : 0.004 0.043 2975 Dihedral : 8.397 114.854 2583 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.66 % Favored : 92.29 % Rotamer: Outliers : 2.26 % Allowed : 23.20 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.18), residues: 2180 helix: -0.94 (0.61), residues: 78 sheet: 0.68 (0.19), residues: 821 loop : -0.82 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 98 TYR 0.030 0.001 TYR E 106 PHE 0.014 0.001 PHE A 509 TRP 0.016 0.001 TRP D 487 HIS 0.004 0.001 HIS E 169 Details of bonding type rmsd covalent geometry : bond 0.00337 (16952) covalent geometry : angle 0.57035 (23192) SS BOND : bond 0.00541 ( 40) SS BOND : angle 0.71299 ( 80) hydrogen bonds : bond 0.02928 ( 505) hydrogen bonds : angle 5.30677 ( 1332) link_BETA1-4 : bond 0.00389 ( 5) link_BETA1-4 : angle 1.84379 ( 15) link_NAG-ASN : bond 0.00529 ( 5) link_NAG-ASN : angle 2.37415 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4796.74 seconds wall clock time: 82 minutes 49.57 seconds (4969.57 seconds total)