Starting phenix.real_space_refine on Fri Mar 22 05:29:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dim_27440/03_2024/8dim_27440.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dim_27440/03_2024/8dim_27440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dim_27440/03_2024/8dim_27440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dim_27440/03_2024/8dim_27440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dim_27440/03_2024/8dim_27440.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dim_27440/03_2024/8dim_27440.pdb" } resolution = 2.62 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= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15825 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 10549 2.51 5 N 2821 2.21 5 O 3297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "D GLU 373": "OE1" <-> "OE2" Residue "D TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 494": "OE1" <-> "OE2" Residue "G TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 494": "OE1" <-> "OE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16745 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3828 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 465} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3824 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 465} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 887 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 903 Chain: "G" Number of atoms: 3824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3824 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 465} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 887 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 903 Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 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: "L" 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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.74, per 1000 atoms: 0.58 Number of scatterers: 16745 At special positions: 0 Unit cell: (132.3, 131.625, 142.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3297 8.00 N 2821 7.00 C 10549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 488 " - pdb=" SG CYS A 492 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 59 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 488 " - pdb=" SG CYS D 492 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 59 " - pdb=" SG CYS G 292 " distance=2.03 Simple disulfide: pdb=" SG CYS G 72 " - pdb=" SG CYS G 84 " distance=2.03 Simple disulfide: pdb=" SG CYS G 107 " - pdb=" SG CYS G 153 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 320 " distance=2.03 Simple disulfide: pdb=" SG CYS G 488 " - pdb=" SG CYS G 492 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A 601 " - " ASN A 28 " " NAG A 602 " - " ASN A 40 " " NAG A 603 " - " ASN A 498 " " NAG D 601 " - " ASN D 28 " " NAG D 602 " - " ASN D 40 " " NAG D 603 " - " ASN D 498 " " NAG G 601 " - " ASN G 28 " " NAG G 602 " - " ASN G 40 " " NAG G 603 " - " ASN G 498 " " NAG J 1 " - " ASN A 104 " " NAG K 1 " - " ASN D 104 " " NAG L 1 " - " ASN G 104 " Time building additional restraints: 6.37 Conformation dependent library (CDL) restraints added in 3.3 seconds 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3898 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 48 sheets defined 18.6% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 81 through 88 removed outlier: 4.118A pdb=" N GLU A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER A 86 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.662A pdb=" N SER A 138 " --> pdb=" O PRO A 135 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 381 through 402 removed outlier: 3.692A pdb=" N THR A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 470 removed outlier: 3.816A pdb=" N GLU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 460 " --> pdb=" O ASP A 456 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 462 " --> pdb=" O ASN A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.643A pdb=" N THR B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 81 through 88 removed outlier: 4.149A pdb=" N GLU D 85 " --> pdb=" O PRO D 82 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N SER D 86 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D 88 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 123 Processing helix chain 'D' and resid 201 through 209 Processing helix chain 'D' and resid 381 through 402 removed outlier: 3.705A pdb=" N THR D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 470 removed outlier: 3.791A pdb=" N GLU D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 462 " --> pdb=" O ASN D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 499 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.672A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 80 Processing helix chain 'G' and resid 81 through 88 removed outlier: 4.162A pdb=" N GLU G 85 " --> pdb=" O PRO G 82 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER G 86 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA G 88 " --> pdb=" O GLU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 123 Processing helix chain 'G' and resid 201 through 209 Processing helix chain 'G' and resid 381 through 402 removed outlier: 3.694A pdb=" N THR G 385 " --> pdb=" O ASP G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 418 through 470 removed outlier: 3.805A pdb=" N GLU G 449 " --> pdb=" O LEU G 445 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS G 460 " --> pdb=" O ASP G 456 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU G 462 " --> pdb=" O ASN G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 499 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.653A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.719A pdb=" N GLU C 84 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.682A pdb=" N GLU F 84 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.723A pdb=" N GLU I 84 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA5, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.591A pdb=" N LEU A 67 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 96 " --> pdb=" O ILE A 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 132 removed outlier: 3.582A pdb=" N SER A 127 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR A 270 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU A 193 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 272 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU A 193 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 125 through 132 removed outlier: 3.582A pdb=" N SER A 127 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR A 270 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU A 193 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 272 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 150 through 155 removed outlier: 4.751A pdb=" N CYS A 153 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 178 through 183 Processing sheet with id=AB1, first strand: chain 'A' and resid 302 through 303 removed outlier: 4.180A pdb=" N CYS A 296 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.525A pdb=" N ILE B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.814A pdb=" N VAL B 110 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 376 through 380 Processing sheet with id=AB6, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=AB7, first strand: chain 'D' and resid 46 through 48 Processing sheet with id=AB8, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB9, first strand: chain 'D' and resid 67 through 68 removed outlier: 6.603A pdb=" N LEU D 67 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE D 96 " --> pdb=" O ILE D 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 125 through 132 removed outlier: 3.595A pdb=" N SER D 127 " --> pdb=" O LYS D 275 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR D 270 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU D 193 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 272 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU D 193 " --> pdb=" O PRO D 268 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 125 through 132 removed outlier: 3.595A pdb=" N SER D 127 " --> pdb=" O LYS D 275 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR D 270 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU D 193 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 272 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 150 through 155 removed outlier: 4.690A pdb=" N CYS D 153 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 178 through 183 Processing sheet with id=AC5, first strand: chain 'D' and resid 302 through 303 removed outlier: 4.184A pdb=" N CYS D 296 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AC7, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.632A pdb=" N VAL E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 92 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.632A pdb=" N VAL E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 92 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL E 110 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 376 through 380 Processing sheet with id=AD1, first strand: chain 'G' and resid 32 through 33 Processing sheet with id=AD2, first strand: chain 'G' and resid 46 through 48 Processing sheet with id=AD3, first strand: chain 'G' and resid 50 through 51 Processing sheet with id=AD4, first strand: chain 'G' and resid 67 through 68 removed outlier: 6.584A pdb=" N LEU G 67 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE G 96 " --> pdb=" O ILE G 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'G' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER G 127 " --> pdb=" O LYS G 275 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR G 270 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU G 193 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE G 272 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU G 193 " --> pdb=" O PRO G 268 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER G 127 " --> pdb=" O LYS G 275 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR G 270 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU G 193 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE G 272 " --> pdb=" O LEU G 191 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 150 through 155 removed outlier: 4.750A pdb=" N CYS G 153 " --> pdb=" O SER G 160 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 178 through 183 Processing sheet with id=AD9, first strand: chain 'G' and resid 302 through 303 removed outlier: 4.187A pdb=" N CYS G 296 " --> pdb=" O ILE G 303 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.555A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.815A pdb=" N VAL H 110 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.574A pdb=" N VAL C 10 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.574A pdb=" N VAL C 10 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AE7, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.605A pdb=" N VAL F 10 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.605A pdb=" N VAL F 10 " --> pdb=" O THR F 109 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 18 through 23 removed outlier: 3.613A pdb=" N SER F 71 " --> pdb=" O SER F 68 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.607A pdb=" N VAL I 10 " --> pdb=" O THR I 109 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.607A pdb=" N VAL I 10 " --> pdb=" O THR I 109 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 18 through 23 removed outlier: 3.623A pdb=" N SER I 71 " --> pdb=" O SER I 68 " (cutoff:3.500A) 660 hydrogen bonds defined for protein. 1746 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: 5.95 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5376 1.35 - 1.47: 4297 1.47 - 1.58: 7349 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 17130 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 BMA L 3 " pdb=" C2 BMA L 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 17125 not shown) Histogram of bond angle deviations from ideal: 97.24 - 104.60: 271 104.60 - 111.95: 8473 111.95 - 119.30: 5623 119.30 - 126.66: 8613 126.66 - 134.01: 311 Bond angle restraints: 23291 Sorted by residual: angle pdb=" C ASP C 51 " pdb=" N ASN C 52 " pdb=" CA ASN C 52 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.17e+00 angle pdb=" C ASP F 51 " pdb=" N ASN F 52 " pdb=" CA ASN F 52 " ideal model delta sigma weight residual 121.54 126.33 -4.79 1.91e+00 2.74e-01 6.28e+00 angle pdb=" C TYR G 209 " pdb=" N GLN G 210 " pdb=" CA GLN G 210 " ideal model delta sigma weight residual 121.54 126.30 -4.76 1.91e+00 2.74e-01 6.20e+00 angle pdb=" C ASP I 51 " pdb=" N ASN I 52 " pdb=" CA ASN I 52 " ideal model delta sigma weight residual 121.54 126.12 -4.58 1.91e+00 2.74e-01 5.76e+00 angle pdb=" C CYS G 292 " pdb=" CA CYS G 292 " pdb=" CB CYS G 292 " ideal model delta sigma weight residual 113.15 108.04 5.11 2.38e+00 1.77e-01 4.61e+00 ... (remaining 23286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.55: 9339 21.55 - 43.09: 816 43.09 - 64.64: 166 64.64 - 86.18: 35 86.18 - 107.73: 15 Dihedral angle restraints: 10371 sinusoidal: 4234 harmonic: 6137 Sorted by residual: dihedral pdb=" CB CYS D 59 " pdb=" SG CYS D 59 " pdb=" SG CYS D 292 " pdb=" CB CYS D 292 " ideal model delta sinusoidal sigma weight residual -86.00 -20.52 -65.48 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" CB CYS G 59 " pdb=" SG CYS G 59 " pdb=" SG CYS G 292 " pdb=" CB CYS G 292 " ideal model delta sinusoidal sigma weight residual -86.00 -20.83 -65.17 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS A 292 " pdb=" CB CYS A 292 " ideal model delta sinusoidal sigma weight residual -86.00 -21.16 -64.84 1 1.00e+01 1.00e-02 5.52e+01 ... (remaining 10368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2129 0.054 - 0.107: 397 0.107 - 0.161: 80 0.161 - 0.215: 0 0.215 - 0.268: 3 Chirality restraints: 2609 Sorted by residual: chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2606 not shown) Planarity restraints: 2987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA I 13 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO I 14 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO I 14 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 14 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 13 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO F 14 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 14 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 14 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 13 " -0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO C 14 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " -0.023 5.00e-02 4.00e+02 ... (remaining 2984 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1194 2.74 - 3.28: 14604 3.28 - 3.82: 25936 3.82 - 4.36: 31856 4.36 - 4.90: 58339 Nonbonded interactions: 131929 Sorted by model distance: nonbonded pdb=" OD2 ASP A 381 " pdb=" OG SER A 384 " model vdw 2.196 2.440 nonbonded pdb=" OD2 ASP D 381 " pdb=" OG SER D 384 " model vdw 2.200 2.440 nonbonded pdb=" OD2 ASP G 381 " pdb=" OG SER G 384 " model vdw 2.204 2.440 nonbonded pdb=" NZ LYS G 60 " pdb=" OD1 ASP G 291 " model vdw 2.222 2.520 nonbonded pdb=" NZ LYS A 60 " pdb=" OD1 ASP A 291 " model vdw 2.222 2.520 ... (remaining 131924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 506 or resid 601 through 603)) selection = chain 'D' selection = chain 'G' } ncs_group { reference = (chain 'B' and (resid 2 through 29 or resid 31 through 119)) selection = (chain 'E' and (resid 2 through 29 or resid 31 through 119)) selection = (chain 'H' and (resid 2 through 29 or resid 31 through 119)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 36.630 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 47.310 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 0.032 17130 Z= 0.202 Angle : 0.555 8.904 23291 Z= 0.283 Chirality : 0.044 0.268 2609 Planarity : 0.004 0.044 2975 Dihedral : 16.979 107.725 6410 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.08 % Favored : 97.64 % Rotamer: Outliers : 3.52 % Allowed : 21.20 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.18), residues: 2117 helix: 2.09 (0.29), residues: 351 sheet: 0.99 (0.21), residues: 579 loop : -0.79 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 92 HIS 0.004 0.001 HIS A 25 PHE 0.014 0.001 PHE A 128 TYR 0.012 0.001 TYR E 95 ARG 0.004 0.000 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 155 time to evaluate : 1.853 Fit side-chains outliers start: 59 outliers final: 55 residues processed: 212 average time/residue: 1.1941 time to fit residues: 284.9083 Evaluate side-chains 204 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 149 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 331 MET Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 495 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 28 ASN Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN D 173 ASN D 290 HIS D 469 GLN G 290 HIS I 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.0494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17130 Z= 0.219 Angle : 0.548 8.770 23291 Z= 0.282 Chirality : 0.044 0.161 2609 Planarity : 0.004 0.037 2975 Dihedral : 8.794 59.408 2766 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.36 % Favored : 97.35 % Rotamer: Outliers : 4.42 % Allowed : 20.47 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.18), residues: 2117 helix: 2.13 (0.29), residues: 357 sheet: 1.05 (0.21), residues: 597 loop : -0.73 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 436 HIS 0.005 0.001 HIS A 25 PHE 0.016 0.002 PHE G 128 TYR 0.014 0.001 TYR C 99 ARG 0.003 0.000 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 157 time to evaluate : 2.063 Fit side-chains REVERT: A 494 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7170 (tp30) REVERT: B 30 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7684 (mtm-85) REVERT: D 172 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: D 188 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7923 (pttt) REVERT: D 494 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7193 (tp30) REVERT: G 129 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: G 172 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: G 355 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: F 66 SER cc_start: 0.7263 (t) cc_final: 0.6811 (p) outliers start: 75 outliers final: 42 residues processed: 213 average time/residue: 1.2444 time to fit residues: 296.9284 Evaluate side-chains 197 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 149 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 0.0980 chunk 128 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 188 optimal weight: 0.0570 chunk 203 optimal weight: 20.0000 chunk 167 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 overall best weight: 2.0304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN D 173 ASN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17130 Z= 0.340 Angle : 0.605 8.790 23291 Z= 0.311 Chirality : 0.046 0.172 2609 Planarity : 0.005 0.041 2975 Dihedral : 7.223 59.393 2733 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.74 % Favored : 96.97 % Rotamer: Outliers : 5.65 % Allowed : 19.24 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.18), residues: 2117 helix: 1.99 (0.28), residues: 357 sheet: 1.16 (0.21), residues: 585 loop : -0.85 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 92 HIS 0.007 0.001 HIS A 25 PHE 0.023 0.002 PHE A 128 TYR 0.017 0.002 TYR H 95 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 131 time to evaluate : 1.901 Fit side-chains revert: symmetry clash REVERT: A 129 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6472 (tt0) REVERT: A 494 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7030 (tp30) REVERT: B 30 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7540 (ptm-80) REVERT: D 172 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: D 188 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8076 (pttt) REVERT: D 494 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7134 (tp30) REVERT: G 129 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7198 (tt0) REVERT: G 172 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: G 188 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7849 (pttt) REVERT: G 310 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.7711 (pt0) REVERT: G 355 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7586 (mt-10) REVERT: F 32 ASP cc_start: 0.6148 (OUTLIER) cc_final: 0.5853 (m-30) outliers start: 97 outliers final: 50 residues processed: 209 average time/residue: 1.2732 time to fit residues: 297.0126 Evaluate side-chains 184 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 124 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 310 GLN Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 20 optimal weight: 0.0000 chunk 89 optimal weight: 0.7980 chunk 126 optimal weight: 0.0010 chunk 188 optimal weight: 0.0670 chunk 200 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 179 optimal weight: 8.9990 chunk 53 optimal weight: 0.0270 overall best weight: 0.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 ASN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17130 Z= 0.118 Angle : 0.454 8.378 23291 Z= 0.236 Chirality : 0.042 0.135 2609 Planarity : 0.004 0.033 2975 Dihedral : 5.824 59.445 2729 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.65 % Favored : 98.06 % Rotamer: Outliers : 3.69 % Allowed : 20.69 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.18), residues: 2117 helix: 2.48 (0.29), residues: 357 sheet: 1.28 (0.20), residues: 639 loop : -0.73 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 436 HIS 0.003 0.000 HIS A 370 PHE 0.009 0.001 PHE E 29 TYR 0.009 0.001 TYR H 95 ARG 0.004 0.000 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 155 time to evaluate : 1.787 Fit side-chains REVERT: A 183 THR cc_start: 0.8145 (t) cc_final: 0.7828 (m) REVERT: A 374 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.6788 (mt0) REVERT: A 494 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7151 (tp30) REVERT: B 30 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.6733 (ptm-80) REVERT: D 172 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: D 319 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: D 374 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.6466 (mt0) REVERT: D 494 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7196 (tp30) REVERT: G 172 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: G 183 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7802 (m) REVERT: G 188 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7689 (pttt) REVERT: G 355 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: G 374 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7005 (mt0) REVERT: F 66 SER cc_start: 0.7339 (t) cc_final: 0.6894 (p) outliers start: 62 outliers final: 29 residues processed: 201 average time/residue: 1.2773 time to fit residues: 286.9655 Evaluate side-chains 179 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 140 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 366 TYR Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain G residue 384 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 5.9990 chunk 113 optimal weight: 0.0270 chunk 2 optimal weight: 0.7980 chunk 148 optimal weight: 0.0030 chunk 82 optimal weight: 2.9990 chunk 170 optimal weight: 0.0870 chunk 138 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.7828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17130 Z= 0.160 Angle : 0.480 8.239 23291 Z= 0.248 Chirality : 0.042 0.143 2609 Planarity : 0.004 0.033 2975 Dihedral : 5.541 59.780 2715 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.22 % Favored : 97.49 % Rotamer: Outliers : 3.97 % Allowed : 20.19 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.18), residues: 2117 helix: 2.60 (0.29), residues: 357 sheet: 1.39 (0.21), residues: 609 loop : -0.67 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 92 HIS 0.004 0.001 HIS A 25 PHE 0.017 0.001 PHE A 128 TYR 0.013 0.001 TYR H 95 ARG 0.002 0.000 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 151 time to evaluate : 1.768 Fit side-chains REVERT: A 129 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6342 (tt0) REVERT: A 183 THR cc_start: 0.8252 (t) cc_final: 0.7839 (m) REVERT: A 374 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.6884 (mt0) REVERT: A 406 GLN cc_start: 0.6855 (OUTLIER) cc_final: 0.6103 (mt0) REVERT: A 494 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7166 (tp30) REVERT: B 30 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7000 (ptm-80) REVERT: D 172 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: D 374 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.6514 (mt0) REVERT: D 494 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7182 (tp30) REVERT: G 129 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: G 172 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: G 188 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7741 (pttt) REVERT: G 355 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7592 (mt-10) REVERT: G 374 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7044 (mt0) REVERT: F 32 ASP cc_start: 0.6183 (OUTLIER) cc_final: 0.5932 (m-30) REVERT: F 66 SER cc_start: 0.7431 (t) cc_final: 0.7060 (p) outliers start: 67 outliers final: 37 residues processed: 206 average time/residue: 1.2475 time to fit residues: 287.4538 Evaluate side-chains 190 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 141 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain G residue 384 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 66 optimal weight: 0.0060 chunk 105 optimal weight: 0.8980 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN B 103 GLN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17130 Z= 0.264 Angle : 0.539 8.290 23291 Z= 0.278 Chirality : 0.044 0.158 2609 Planarity : 0.004 0.037 2975 Dihedral : 5.695 58.885 2715 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.55 % Favored : 97.16 % Rotamer: Outliers : 4.08 % Allowed : 20.41 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.18), residues: 2117 helix: 2.37 (0.28), residues: 357 sheet: 1.30 (0.21), residues: 579 loop : -0.66 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 92 HIS 0.006 0.001 HIS A 25 PHE 0.022 0.002 PHE D 128 TYR 0.016 0.001 TYR H 95 ARG 0.003 0.000 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 131 time to evaluate : 1.800 Fit side-chains revert: symmetry clash REVERT: A 129 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6373 (tt0) REVERT: A 374 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7037 (mt0) REVERT: A 406 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6094 (mt0) REVERT: A 494 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7127 (tp30) REVERT: B 30 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.6744 (ptm-80) REVERT: D 172 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6755 (mp0) REVERT: D 374 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.6661 (mt0) REVERT: D 494 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7154 (tp30) REVERT: G 129 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7204 (tt0) REVERT: G 172 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: G 188 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7828 (pttt) REVERT: G 355 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: G 374 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7184 (mt0) REVERT: F 32 ASP cc_start: 0.6155 (OUTLIER) cc_final: 0.5954 (m-30) outliers start: 69 outliers final: 42 residues processed: 188 average time/residue: 1.3008 time to fit residues: 272.4943 Evaluate side-chains 183 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 129 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain G residue 384 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 168 optimal weight: 0.1980 chunk 111 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17130 Z= 0.189 Angle : 0.500 8.156 23291 Z= 0.260 Chirality : 0.043 0.156 2609 Planarity : 0.004 0.036 2975 Dihedral : 5.579 58.567 2715 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.51 % Favored : 97.30 % Rotamer: Outliers : 4.42 % Allowed : 20.69 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.18), residues: 2117 helix: 2.42 (0.28), residues: 357 sheet: 1.28 (0.21), residues: 579 loop : -0.67 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 92 HIS 0.004 0.001 HIS A 25 PHE 0.017 0.001 PHE A 128 TYR 0.013 0.001 TYR H 95 ARG 0.002 0.000 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 128 time to evaluate : 1.883 Fit side-chains REVERT: A 129 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6366 (tt0) REVERT: A 374 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7030 (mt0) REVERT: A 406 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.6094 (mt0) REVERT: A 494 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7131 (tp30) REVERT: B 30 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7644 (ptm-80) REVERT: D 172 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: D 374 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.6659 (mt0) REVERT: D 494 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7160 (tp30) REVERT: G 129 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7203 (tt0) REVERT: G 172 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: G 188 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7793 (pttt) REVERT: G 355 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: G 374 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7188 (mt0) REVERT: F 32 ASP cc_start: 0.6166 (OUTLIER) cc_final: 0.5924 (m-30) outliers start: 75 outliers final: 48 residues processed: 192 average time/residue: 1.3523 time to fit residues: 288.6458 Evaluate side-chains 190 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 130 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 374 GLN Chi-restraints excluded: chain G residue 384 SER Chi-restraints excluded: chain G residue 495 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 126 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17130 Z= 0.195 Angle : 0.500 8.067 23291 Z= 0.259 Chirality : 0.043 0.154 2609 Planarity : 0.004 0.036 2975 Dihedral : 5.521 58.409 2715 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.46 % Favored : 97.40 % Rotamer: Outliers : 4.25 % Allowed : 21.03 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.18), residues: 2117 helix: 2.44 (0.28), residues: 357 sheet: 1.23 (0.21), residues: 594 loop : -0.69 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 92 HIS 0.004 0.001 HIS A 25 PHE 0.018 0.002 PHE A 128 TYR 0.013 0.001 TYR H 95 ARG 0.002 0.000 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 132 time to evaluate : 1.718 Fit side-chains revert: symmetry clash REVERT: A 129 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6344 (tt0) REVERT: A 374 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7054 (mt0) REVERT: A 406 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6096 (mt0) REVERT: A 494 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7136 (tp30) REVERT: D 172 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: D 374 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.6691 (mt0) REVERT: D 494 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7159 (tp30) REVERT: G 129 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: G 172 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: G 188 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7792 (pttt) REVERT: G 355 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: G 373 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7160 (pm20) REVERT: F 32 ASP cc_start: 0.6167 (OUTLIER) cc_final: 0.5927 (m-30) outliers start: 72 outliers final: 47 residues processed: 192 average time/residue: 1.3455 time to fit residues: 287.1232 Evaluate side-chains 189 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 131 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 384 SER Chi-restraints excluded: chain G residue 495 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 80 optimal weight: 0.1980 chunk 145 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17130 Z= 0.269 Angle : 0.542 8.093 23291 Z= 0.280 Chirality : 0.044 0.162 2609 Planarity : 0.004 0.037 2975 Dihedral : 5.556 58.589 2711 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.65 % Favored : 97.21 % Rotamer: Outliers : 4.08 % Allowed : 21.20 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.18), residues: 2117 helix: 2.31 (0.28), residues: 357 sheet: 1.22 (0.21), residues: 579 loop : -0.74 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 92 HIS 0.006 0.001 HIS A 25 PHE 0.020 0.002 PHE A 128 TYR 0.016 0.001 TYR H 95 ARG 0.002 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 128 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6405 (tt0) REVERT: A 374 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7187 (mt0) REVERT: A 406 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6155 (mt0) REVERT: A 494 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7061 (tp30) REVERT: D 129 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: D 172 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: D 374 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.6775 (mt0) REVERT: D 494 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7085 (tp30) REVERT: G 129 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: G 172 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: G 188 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7848 (pttt) REVERT: G 355 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7594 (mt-10) REVERT: G 373 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7200 (pm20) outliers start: 69 outliers final: 51 residues processed: 186 average time/residue: 1.3180 time to fit residues: 273.3838 Evaluate side-chains 189 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 127 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 384 SER Chi-restraints excluded: chain G residue 495 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 0.9990 chunk 119 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 206 optimal weight: 0.5980 chunk 189 optimal weight: 20.0000 chunk 164 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 130 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.002 0.025 17130 Z= 0.139 Angle : 0.466 8.043 23291 Z= 0.243 Chirality : 0.042 0.157 2609 Planarity : 0.004 0.035 2975 Dihedral : 5.250 59.524 2711 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.03 % Favored : 97.83 % Rotamer: Outliers : 3.41 % Allowed : 21.87 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.18), residues: 2117 helix: 2.55 (0.28), residues: 357 sheet: 1.24 (0.20), residues: 639 loop : -0.76 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 92 HIS 0.003 0.001 HIS A 25 PHE 0.013 0.001 PHE G 128 TYR 0.010 0.001 TYR B 95 ARG 0.002 0.000 ARG D 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 135 time to evaluate : 1.936 Fit side-chains REVERT: A 129 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6341 (tt0) REVERT: A 406 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6086 (mt0) REVERT: A 494 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7155 (tp30) REVERT: D 172 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: D 374 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.6656 (mt0) REVERT: D 494 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7155 (tp30) REVERT: G 129 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7177 (tt0) REVERT: G 172 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: G 188 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7747 (pttt) REVERT: G 355 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: G 373 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7189 (pm20) REVERT: F 62 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6770 (ptm160) REVERT: I 61 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7107 (t70) outliers start: 57 outliers final: 38 residues processed: 183 average time/residue: 1.3587 time to fit residues: 277.3878 Evaluate side-chains 181 residues out of total 1822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 132 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 406 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain G residue 21 CYS Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 147 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 188 LYS Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain G residue 292 CYS Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 373 GLU Chi-restraints excluded: chain G residue 384 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 168 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 144 optimal weight: 0.0970 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN D 290 HIS D 469 GLN G 173 ASN G 290 HIS F 52 ASN I 52 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.140853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098799 restraints weight = 19340.694| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.50 r_work: 0.3003 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17130 Z= 0.287 Angle : 0.554 7.820 23291 Z= 0.287 Chirality : 0.045 0.165 2609 Planarity : 0.004 0.037 2975 Dihedral : 5.503 59.351 2711 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.84 % Favored : 97.02 % Rotamer: Outliers : 3.69 % Allowed : 21.64 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2117 helix: 2.30 (0.28), residues: 357 sheet: 1.19 (0.21), residues: 600 loop : -0.78 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 92 HIS 0.006 0.001 HIS A 25 PHE 0.022 0.002 PHE A 128 TYR 0.017 0.001 TYR H 95 ARG 0.006 0.000 ARG A 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6668.96 seconds wall clock time: 119 minutes 12.17 seconds (7152.17 seconds total)