Starting phenix.real_space_refine on Thu May 29 06:16:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgv_41245/05_2025/8tgv_41245_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgv_41245/05_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_41245/05_2025/8tgv_41245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgv_41245/05_2025/8tgv_41245.map" model { file = "/net/cci-nas-00/data/ceres_data/8tgv_41245/05_2025/8tgv_41245_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgv_41245/05_2025/8tgv_41245_trim.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} 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: {'GLN:plan1': 3, 'ARG:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ASP: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, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} 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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR: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, 'GLU:plan': 2, 'ARG: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: 14.60, per 1000 atoms: 0.46 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: 8.42 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 3.30 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: 11.60 Time building geometry restraints manager: 9.88 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: 1.040 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: 0.550 Extract box with map and model: 1.150 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 63.910 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.170 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP E 36 HIS 0.003 0.001 HIS E 169 PHE 0.009 0.001 PHE L 138 TYR 0.013 0.001 TYR I 80 ARG 0.020 0.000 ARG A 521 Details of bonding type rmsd link_NAG-ASN : bond 0.00645 ( 5) link_NAG-ASN : angle 2.37339 ( 15) link_BETA1-4 : bond 0.00998 ( 5) link_BETA1-4 : angle 3.78055 ( 15) hydrogen bonds : bond 0.27196 ( 505) hydrogen bonds : angle 9.61585 ( 1332) SS BOND : bond 0.00235 ( 40) SS BOND : angle 0.51534 ( 80) covalent geometry : bond 0.00322 (16952) covalent geometry : angle 0.54463 (23192) *********************** 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 : 2.767 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: A 455 ARG cc_start: 0.8531 (mtp180) cc_final: 0.8223 (mtp-110) 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: 0.5654 time to fit residues: 157.5986 Evaluate side-chains 178 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 2.249 ------------------------------------------------------------------------------- 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 185 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.171144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117610 restraints weight = 73545.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121911 restraints weight = 46724.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121576 restraints weight = 30272.267| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17002 Z= 0.175 Angle : 0.617 7.071 23302 Z= 0.314 Chirality : 0.045 0.264 2643 Planarity : 0.004 0.046 2975 Dihedral : 10.874 115.865 2587 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.94 % Favored : 92.02 % Rotamer: Outliers : 1.62 % Allowed : 21.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2180 helix: -1.05 (0.58), residues: 90 sheet: 0.75 (0.19), residues: 827 loop : -0.98 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 159 HIS 0.004 0.001 HIS E 169 PHE 0.016 0.001 PHE L 208 TYR 0.017 0.001 TYR I 80 ARG 0.006 0.000 ARG A 521 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 5) link_NAG-ASN : angle 2.47562 ( 15) link_BETA1-4 : bond 0.00646 ( 5) link_BETA1-4 : angle 2.45654 ( 15) hydrogen bonds : bond 0.04992 ( 505) hydrogen bonds : angle 6.97014 ( 1332) SS BOND : bond 0.00378 ( 40) SS BOND : angle 0.77018 ( 80) covalent geometry : bond 0.00407 (16952) covalent geometry : angle 0.60990 (23192) *********************** 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 218 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 2.496 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 455 ARG cc_start: 0.8610 (mtp180) cc_final: 0.8093 (tpp-160) REVERT: J 91 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7042 (p0) REVERT: J 123 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7729 (mt0) REVERT: K 48 MET cc_start: 0.7377 (ppp) cc_final: 0.6610 (ppp) outliers start: 28 outliers final: 17 residues processed: 212 average time/residue: 0.5266 time to fit residues: 173.9116 Evaluate side-chains 190 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 2.452 ------------------------------------------------------------------------------- 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 65 ASN Chi-restraints excluded: chain F residue 73 THR 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 70 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 205 THR 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 69 THR 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 19 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.171642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.115793 restraints weight = 74234.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119584 restraints weight = 45271.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121507 restraints weight = 33322.001| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17002 Z= 0.137 Angle : 0.585 8.123 23302 Z= 0.293 Chirality : 0.044 0.262 2643 Planarity : 0.004 0.045 2975 Dihedral : 10.530 114.899 2587 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.52 % Favored : 92.43 % Rotamer: Outliers : 1.57 % Allowed : 22.33 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.18), residues: 2180 helix: -1.22 (0.58), residues: 84 sheet: 0.70 (0.18), residues: 828 loop : -0.95 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 159 HIS 0.003 0.001 HIS G 445 PHE 0.012 0.001 PHE L 208 TYR 0.012 0.001 TYR F 48 ARG 0.004 0.000 ARG A 521 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 5) link_NAG-ASN : angle 2.43087 ( 15) link_BETA1-4 : bond 0.00530 ( 5) link_BETA1-4 : angle 2.36018 ( 15) hydrogen bonds : bond 0.04415 ( 505) hydrogen bonds : angle 6.43227 ( 1332) SS BOND : bond 0.00332 ( 40) SS BOND : angle 0.61372 ( 80) covalent geometry : bond 0.00323 (16952) covalent geometry : angle 0.57904 (23192) *********************** 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 210 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 2.552 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: symmetry clash REVERT: A 455 ARG cc_start: 0.8608 (mtp180) cc_final: 0.8278 (mtp-110) REVERT: F 159 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: I 65 GLN cc_start: 0.8378 (pp30) cc_final: 0.7883 (pp30) REVERT: J 91 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.6992 (p0) REVERT: K 48 MET cc_start: 0.7453 (ppp) cc_final: 0.6879 (ppp) REVERT: L 107 ARG cc_start: 0.7420 (tpt-90) cc_final: 0.7154 (tpt-90) outliers start: 27 outliers final: 22 residues processed: 202 average time/residue: 0.5470 time to fit residues: 173.1551 Evaluate side-chains 199 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 2.501 ------------------------------------------------------------------------------- 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 F residue 51 SER 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 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 203 VAL Chi-restraints excluded: chain C residue 68 ASN 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 13 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN G 445 HIS J 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.170559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116545 restraints weight = 73973.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120814 restraints weight = 46051.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.120360 restraints weight = 29168.802| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1305 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= 0.166 Angle : 0.591 9.126 23302 Z= 0.296 Chirality : 0.045 0.264 2643 Planarity : 0.004 0.046 2975 Dihedral : 10.110 113.361 2585 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.49 % Favored : 91.47 % Rotamer: Outliers : 2.61 % Allowed : 22.16 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2180 helix: -1.16 (0.59), residues: 84 sheet: 0.60 (0.18), residues: 823 loop : -0.96 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 159 HIS 0.004 0.001 HIS E 169 PHE 0.014 0.001 PHE L 208 TYR 0.017 0.001 TYR F 48 ARG 0.003 0.000 ARG A 521 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 5) link_NAG-ASN : angle 2.40595 ( 15) link_BETA1-4 : bond 0.00524 ( 5) link_BETA1-4 : angle 2.36390 ( 15) hydrogen bonds : bond 0.03840 ( 505) hydrogen bonds : angle 6.14657 ( 1332) SS BOND : bond 0.00330 ( 40) SS BOND : angle 0.64247 ( 80) covalent geometry : bond 0.00395 (16952) covalent geometry : angle 0.58525 (23192) *********************** 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 221 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 2.548 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 455 ARG cc_start: 0.8698 (mtp180) cc_final: 0.8364 (mtp-110) REVERT: A 631 MET cc_start: 0.7276 (tpp) cc_final: 0.6964 (tpp) REVERT: F 159 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: I 65 GLN cc_start: 0.8391 (pp30) cc_final: 0.7904 (pp30) REVERT: J 91 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.7378 (p0) REVERT: J 123 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: K 48 MET cc_start: 0.7291 (ppp) cc_final: 0.6740 (ppp) REVERT: L 107 ARG cc_start: 0.7456 (tpt-90) cc_final: 0.7243 (tpt-90) outliers start: 45 outliers final: 35 residues processed: 212 average time/residue: 0.5221 time to fit residues: 173.8265 Evaluate side-chains 205 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 2.439 ------------------------------------------------------------------------------- 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 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 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 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 87 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 J residue 123 GLN Chi-restraints excluded: chain K residue 64 PHE 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 132 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 218 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.170834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.118124 restraints weight = 74051.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120422 restraints weight = 44664.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120453 restraints weight = 33489.864| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1393 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= 0.148 Angle : 0.585 9.861 23302 Z= 0.291 Chirality : 0.044 0.264 2643 Planarity : 0.004 0.046 2975 Dihedral : 9.897 113.983 2585 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.89 % Favored : 92.06 % Rotamer: Outliers : 2.49 % Allowed : 22.16 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2180 helix: -1.05 (0.61), residues: 78 sheet: 0.60 (0.18), residues: 821 loop : -0.94 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 159 HIS 0.004 0.001 HIS E 169 PHE 0.014 0.001 PHE L 208 TYR 0.013 0.001 TYR F 48 ARG 0.002 0.000 ARG I 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 5) link_NAG-ASN : angle 2.40308 ( 15) link_BETA1-4 : bond 0.00509 ( 5) link_BETA1-4 : angle 2.38540 ( 15) hydrogen bonds : bond 0.03561 ( 505) hydrogen bonds : angle 5.98848 ( 1332) SS BOND : bond 0.00318 ( 40) SS BOND : angle 0.61551 ( 80) covalent geometry : bond 0.00353 (16952) covalent geometry : angle 0.57933 (23192) *********************** 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 216 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 2.529 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 455 ARG cc_start: 0.8678 (mtp180) cc_final: 0.8347 (mtp-110) REVERT: F 159 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: F 160 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: D 555 MET cc_start: 0.7756 (tpp) cc_final: 0.7320 (tpt) REVERT: I 10 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8030 (pp20) REVERT: I 59 MET cc_start: 0.6373 (mtp) cc_final: 0.6059 (mtp) REVERT: I 65 GLN cc_start: 0.8256 (pp30) cc_final: 0.7852 (pp30) REVERT: J 91 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.7458 (p0) REVERT: K 48 MET cc_start: 0.7020 (ppp) cc_final: 0.6625 (ppp) REVERT: L 107 ARG cc_start: 0.7334 (tpt-90) cc_final: 0.7042 (tpt170) outliers start: 43 outliers final: 37 residues processed: 208 average time/residue: 0.5194 time to fit residues: 170.4071 Evaluate side-chains 210 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 2.487 ------------------------------------------------------------------------------- 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 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 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 173 SER 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 I residue 183 LEU Chi-restraints excluded: chain J residue 62 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 20 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 219 optimal weight: 0.3980 chunk 155 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.171704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.115983 restraints weight = 73806.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119934 restraints weight = 45426.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121801 restraints weight = 32589.665| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1538 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= 0.115 Angle : 0.568 10.905 23302 Z= 0.279 Chirality : 0.044 0.263 2643 Planarity : 0.004 0.043 2975 Dihedral : 9.473 114.145 2585 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.39 % Favored : 92.57 % Rotamer: Outliers : 2.20 % Allowed : 22.74 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2180 helix: -0.99 (0.60), residues: 78 sheet: 0.63 (0.18), residues: 822 loop : -0.85 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 554 HIS 0.003 0.001 HIS E 169 PHE 0.011 0.001 PHE L 208 TYR 0.010 0.001 TYR A 611 ARG 0.002 0.000 ARG K 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 5) link_NAG-ASN : angle 2.40471 ( 15) link_BETA1-4 : bond 0.00446 ( 5) link_BETA1-4 : angle 2.46183 ( 15) hydrogen bonds : bond 0.03153 ( 505) hydrogen bonds : angle 5.73109 ( 1332) SS BOND : bond 0.00304 ( 40) SS BOND : angle 0.56410 ( 80) covalent geometry : bond 0.00277 (16952) covalent geometry : angle 0.56175 (23192) *********************** 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 223 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 2.790 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 455 ARG cc_start: 0.8691 (mtp180) cc_final: 0.8371 (mtp-110) REVERT: A 493 GLN cc_start: 0.7655 (mp10) cc_final: 0.6474 (tp40) REVERT: F 91 ASP cc_start: 0.7524 (t0) cc_final: 0.7286 (t0) REVERT: F 159 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: I 65 GLN cc_start: 0.8242 (pp30) cc_final: 0.7779 (pp30) REVERT: J 91 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.7298 (p0) REVERT: K 48 MET cc_start: 0.7257 (ppp) cc_final: 0.6853 (ppp) REVERT: L 107 ARG cc_start: 0.7359 (tpt-90) cc_final: 0.7102 (tpt170) outliers start: 38 outliers final: 33 residues processed: 217 average time/residue: 0.5223 time to fit residues: 177.2667 Evaluate side-chains 209 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 2.556 ------------------------------------------------------------------------------- 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 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 213 ASP 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 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 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 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 9 optimal weight: 0.3980 chunk 190 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN K 202 ASN L 146 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.170433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.114704 restraints weight = 73843.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118425 restraints weight = 47149.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119859 restraints weight = 33659.257| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17002 Z= 0.159 Angle : 0.589 10.235 23302 Z= 0.291 Chirality : 0.044 0.258 2643 Planarity : 0.004 0.043 2975 Dihedral : 9.048 113.658 2585 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.12 % Favored : 91.83 % Rotamer: Outliers : 2.61 % Allowed : 22.45 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2180 helix: -0.97 (0.61), residues: 78 sheet: 0.59 (0.18), residues: 816 loop : -0.91 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 109 HIS 0.004 0.001 HIS E 169 PHE 0.014 0.001 PHE L 208 TYR 0.018 0.001 TYR F 48 ARG 0.003 0.000 ARG K 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 5) link_NAG-ASN : angle 2.41934 ( 15) link_BETA1-4 : bond 0.00388 ( 5) link_BETA1-4 : angle 2.68845 ( 15) hydrogen bonds : bond 0.03291 ( 505) hydrogen bonds : angle 5.70880 ( 1332) SS BOND : bond 0.00313 ( 40) SS BOND : angle 0.64273 ( 80) covalent geometry : bond 0.00381 (16952) covalent geometry : angle 0.58225 (23192) *********************** 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 219 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 2.490 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 455 ARG cc_start: 0.8757 (mtp180) cc_final: 0.8429 (mtp-110) REVERT: A 493 GLN cc_start: 0.7768 (mp10) cc_final: 0.6551 (tp40) REVERT: F 91 ASP cc_start: 0.7596 (t0) cc_final: 0.7361 (t0) REVERT: F 159 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7893 (mt0) REVERT: I 65 GLN cc_start: 0.8360 (pp30) cc_final: 0.7931 (pp30) REVERT: J 91 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.7384 (p0) REVERT: K 48 MET cc_start: 0.7445 (ppp) cc_final: 0.7071 (ppp) REVERT: K 213 ASP cc_start: 0.7655 (m-30) cc_final: 0.7367 (m-30) REVERT: L 107 ARG cc_start: 0.7423 (tpt-90) cc_final: 0.7177 (tpt170) outliers start: 45 outliers final: 41 residues processed: 212 average time/residue: 0.5068 time to fit residues: 168.7065 Evaluate side-chains 213 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 2.685 ------------------------------------------------------------------------------- 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 481 ASP 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 51 SER 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 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 181 optimal weight: 0.0670 chunk 49 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 197 optimal weight: 0.0870 chunk 147 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 180 optimal weight: 0.4980 chunk 105 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.171888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.130766 restraints weight = 74615.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128273 restraints weight = 94631.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.131490 restraints weight = 71461.952| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17002 Z= 0.102 Angle : 0.574 16.360 23302 Z= 0.283 Chirality : 0.044 0.258 2643 Planarity : 0.004 0.041 2975 Dihedral : 8.819 114.245 2585 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.44 % Allowed : 22.74 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.18), residues: 2180 helix: -0.86 (0.61), residues: 78 sheet: 0.63 (0.19), residues: 821 loop : -0.83 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 159 HIS 0.003 0.001 HIS E 169 PHE 0.009 0.001 PHE L 208 TYR 0.011 0.001 TYR A 611 ARG 0.004 0.000 ARG K 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 5) link_NAG-ASN : angle 2.49707 ( 15) link_BETA1-4 : bond 0.00413 ( 5) link_BETA1-4 : angle 2.24803 ( 15) hydrogen bonds : bond 0.02926 ( 505) hydrogen bonds : angle 5.52055 ( 1332) SS BOND : bond 0.00318 ( 40) SS BOND : angle 0.74066 ( 80) covalent geometry : bond 0.00244 (16952) covalent geometry : angle 0.56760 (23192) *********************** 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 218 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 2.599 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 455 ARG cc_start: 0.8743 (mtp180) cc_final: 0.8398 (mtp-110) REVERT: A 493 GLN cc_start: 0.7359 (mp10) cc_final: 0.6314 (tp40) REVERT: F 91 ASP cc_start: 0.7555 (t0) cc_final: 0.7258 (t0) REVERT: F 159 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7691 (mt0) REVERT: D 555 MET cc_start: 0.7281 (tpp) cc_final: 0.6877 (tpt) REVERT: I 65 GLN cc_start: 0.8410 (pp30) cc_final: 0.7958 (pp30) REVERT: J 91 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.7480 (p0) REVERT: K 48 MET cc_start: 0.6721 (ppp) cc_final: 0.6408 (ppp) REVERT: K 213 ASP cc_start: 0.7627 (m-30) cc_final: 0.7323 (m-30) outliers start: 42 outliers final: 37 residues processed: 213 average time/residue: 0.5239 time to fit residues: 173.8442 Evaluate side-chains 211 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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 481 ASP Chi-restraints excluded: chain A residue 620 CYS 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 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 74 ILE 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 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 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 I residue 183 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 212 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 187 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.170167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113798 restraints weight = 74168.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118531 restraints weight = 44597.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.120239 restraints weight = 31201.311| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 17002 Z= 0.103 Angle : 0.574 22.359 23302 Z= 0.281 Chirality : 0.044 0.257 2643 Planarity : 0.004 0.042 2975 Dihedral : 8.672 114.427 2585 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.06 % Favored : 92.89 % Rotamer: Outliers : 2.44 % Allowed : 22.85 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2180 helix: -0.85 (0.61), residues: 78 sheet: 0.66 (0.19), residues: 821 loop : -0.81 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 159 HIS 0.002 0.001 HIS E 169 PHE 0.009 0.001 PHE L 208 TYR 0.019 0.001 TYR I 32 ARG 0.003 0.000 ARG K 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 5) link_NAG-ASN : angle 2.42184 ( 15) link_BETA1-4 : bond 0.00407 ( 5) link_BETA1-4 : angle 1.95971 ( 15) hydrogen bonds : bond 0.02849 ( 505) hydrogen bonds : angle 5.39233 ( 1332) SS BOND : bond 0.00389 ( 40) SS BOND : angle 0.74635 ( 80) covalent geometry : bond 0.00249 (16952) covalent geometry : angle 0.56829 (23192) *********************** 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 221 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 2.472 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 455 ARG cc_start: 0.8668 (mtp180) cc_final: 0.8350 (mtp-110) REVERT: A 493 GLN cc_start: 0.7587 (mp10) cc_final: 0.6402 (tp40) REVERT: F 91 ASP cc_start: 0.7480 (t0) cc_final: 0.7247 (t0) REVERT: F 159 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: J 91 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7252 (p0) REVERT: K 48 MET cc_start: 0.7282 (ppp) cc_final: 0.6844 (ppp) REVERT: K 213 ASP cc_start: 0.7606 (m-30) cc_final: 0.7300 (m-30) outliers start: 42 outliers final: 40 residues processed: 215 average time/residue: 0.5171 time to fit residues: 174.8177 Evaluate side-chains 218 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 2.654 ------------------------------------------------------------------------------- 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 481 ASP Chi-restraints excluded: chain A residue 620 CYS 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 51 SER 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 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 156 THR 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 I residue 183 LEU Chi-restraints excluded: chain J residue 62 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 99 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 63 optimal weight: 20.0000 chunk 114 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.169688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.127873 restraints weight = 74139.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122517 restraints weight = 84604.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126434 restraints weight = 66688.863| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17002 Z= 0.166 Angle : 0.603 23.701 23302 Z= 0.299 Chirality : 0.044 0.255 2643 Planarity : 0.004 0.042 2975 Dihedral : 8.582 114.431 2585 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.67 % Favored : 91.28 % Rotamer: Outliers : 2.44 % Allowed : 23.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2180 helix: -0.87 (0.61), residues: 78 sheet: 0.58 (0.19), residues: 821 loop : -0.89 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 109 HIS 0.005 0.001 HIS E 169 PHE 0.016 0.001 PHE G 447 TYR 0.019 0.001 TYR F 48 ARG 0.005 0.000 ARG K 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 5) link_NAG-ASN : angle 2.37513 ( 15) link_BETA1-4 : bond 0.00377 ( 5) link_BETA1-4 : angle 1.94120 ( 15) hydrogen bonds : bond 0.03142 ( 505) hydrogen bonds : angle 5.47684 ( 1332) SS BOND : bond 0.00352 ( 40) SS BOND : angle 0.70313 ( 80) covalent geometry : bond 0.00399 (16952) covalent geometry : angle 0.59839 (23192) ********************** 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 217 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 2.869 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 455 ARG cc_start: 0.8899 (mtp180) cc_final: 0.8550 (mtp-110) REVERT: A 493 GLN cc_start: 0.7728 (mp10) cc_final: 0.6566 (tp40) REVERT: F 91 ASP cc_start: 0.7598 (t0) cc_final: 0.7303 (t0) REVERT: F 159 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: J 80 MET cc_start: 0.7225 (tpp) cc_final: 0.6983 (tpt) REVERT: J 91 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.7540 (p0) REVERT: K 48 MET cc_start: 0.7095 (ppp) cc_final: 0.6691 (ppp) outliers start: 42 outliers final: 40 residues processed: 211 average time/residue: 0.5163 time to fit residues: 170.5172 Evaluate side-chains 214 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 2.496 ------------------------------------------------------------------------------- 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 481 ASP 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 51 SER 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 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 73 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 114 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 110 optimal weight: 0.1980 chunk 125 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** 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 = 0.4145 r_free = 0.4145 target = 0.169854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.129438 restraints weight = 74267.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128003 restraints weight = 97783.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130640 restraints weight = 73044.359| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17002 Z= 0.125 Angle : 0.586 23.442 23302 Z= 0.288 Chirality : 0.044 0.255 2643 Planarity : 0.004 0.041 2975 Dihedral : 8.452 114.961 2583 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.29 % Favored : 92.66 % Rotamer: Outliers : 2.32 % Allowed : 23.20 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2180 helix: -0.78 (0.61), residues: 78 sheet: 0.58 (0.19), residues: 823 loop : -0.86 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 159 HIS 0.003 0.001 HIS E 169 PHE 0.011 0.001 PHE L 208 TYR 0.012 0.001 TYR F 48 ARG 0.004 0.000 ARG K 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 5) link_NAG-ASN : angle 2.40761 ( 15) link_BETA1-4 : bond 0.00381 ( 5) link_BETA1-4 : angle 1.82324 ( 15) hydrogen bonds : bond 0.02921 ( 505) hydrogen bonds : angle 5.39175 ( 1332) SS BOND : bond 0.00418 ( 40) SS BOND : angle 0.63374 ( 80) covalent geometry : bond 0.00301 (16952) covalent geometry : angle 0.58137 (23192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8427.13 seconds wall clock time: 146 minutes 37.44 seconds (8797.44 seconds total)