Starting phenix.real_space_refine on Thu Mar 21 04:38:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfo_25878/03_2024/7tfo_25878.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfo_25878/03_2024/7tfo_25878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfo_25878/03_2024/7tfo_25878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfo_25878/03_2024/7tfo_25878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfo_25878/03_2024/7tfo_25878.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfo_25878/03_2024/7tfo_25878.pdb" } resolution = 4.1 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= 0.002 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 11499 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 113 5.16 5 C 11219 2.51 5 N 3040 2.21 5 O 3402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 81": "OD1" <-> "OD2" Residue "P TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 85": "OD1" <-> "OD2" Residue "Q TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 648": "OE1" <-> "OE2" Residue "Y GLU 584": "OE1" <-> "OE2" Residue "Y GLU 648": "OE1" <-> "OE2" Residue "Z PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17774 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3245 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 10 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3175 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 20, 'TRANS': 390} Chain breaks: 10 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3110 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 21, 'TRANS': 382} Chain breaks: 8 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 914 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 905 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 828 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 103} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 834 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "X" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "Y" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 917 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Z" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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: "F" 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: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.56, per 1000 atoms: 0.54 Number of scatterers: 17774 At special positions: 0 Unit cell: (128.744, 122.056, 141.284, 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 113 16.00 O 3402 8.00 N 3040 7.00 C 11219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=1.68 Simple disulfide: pdb=" SG CYS X 598 " - pdb=" SG CYS X 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 598 " - pdb=" SG CYS Y 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 604 " 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A 601 " - " ASN A 197 " " NAG B 601 " - " ASN B 276 " " NAG B 602 " - " ASN B 363 " " NAG C 601 " - " ASN C 197 " " NAG C 602 " - " ASN C 363 " " NAG D 1 " - " ASN A 386 " " NAG E 1 " - " ASN A 363 " " NAG F 1 " - " ASN A 276 " " NAG G 1 " - " ASN A 262 " " NAG K 1 " - " ASN C 276 " Time building additional restraints: 7.14 Conformation dependent library (CDL) restraints added in 3.4 seconds 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4210 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 39 sheets defined 20.7% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.579A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.818A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 57 through 61 removed outlier: 4.305A pdb=" N TYR B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.542A pdb=" N HIS B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 removed outlier: 4.242A pdb=" N THR B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 354 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.516A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 115 removed outlier: 3.649A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 334 through 350 removed outlier: 3.609A pdb=" N LYS C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.904A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 483 removed outlier: 4.094A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'L' and resid 27 through 31 removed outlier: 3.718A pdb=" N SER L 31 " --> pdb=" O PHE L 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.784A pdb=" N THR P 87 " --> pdb=" O SER P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 100A removed outlier: 3.929A pdb=" N SER P 100A" --> pdb=" O ARG P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27A through 30 removed outlier: 4.022A pdb=" N GLU Q 29 " --> pdb=" O SER Q 27A" (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'X' and resid 515 through 522 removed outlier: 3.588A pdb=" N PHE X 519 " --> pdb=" O ILE X 515 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU X 520 " --> pdb=" O GLY X 516 " (cutoff:3.500A) Processing helix chain 'X' and resid 529 through 541 removed outlier: 3.784A pdb=" N MET X 535 " --> pdb=" O GLY X 531 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR X 538 " --> pdb=" O SER X 534 " (cutoff:3.500A) Processing helix chain 'X' and resid 564 through 596 removed outlier: 3.522A pdb=" N LYS X 574 " --> pdb=" O VAL X 570 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG X 579 " --> pdb=" O GLN X 575 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP X 596 " --> pdb=" O LEU X 592 " (cutoff:3.500A) Processing helix chain 'X' and resid 620 through 624 removed outlier: 3.741A pdb=" N TRP X 623 " --> pdb=" O SER X 620 " (cutoff:3.500A) Processing helix chain 'X' and resid 627 through 636 Processing helix chain 'X' and resid 638 through 656 removed outlier: 3.716A pdb=" N GLU X 648 " --> pdb=" O GLY X 644 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER X 649 " --> pdb=" O LEU X 645 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN X 653 " --> pdb=" O SER X 649 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS X 655 " --> pdb=" O ASN X 651 " (cutoff:3.500A) Processing helix chain 'Y' and resid 529 through 536 removed outlier: 3.515A pdb=" N THR Y 536 " --> pdb=" O ALA Y 532 " (cutoff:3.500A) Processing helix chain 'Y' and resid 540 through 545 removed outlier: 4.048A pdb=" N LEU Y 545 " --> pdb=" O ARG Y 542 " (cutoff:3.500A) Processing helix chain 'Y' and resid 564 through 596 removed outlier: 3.744A pdb=" N TRP Y 596 " --> pdb=" O LEU Y 592 " (cutoff:3.500A) Processing helix chain 'Y' and resid 618 through 623 removed outlier: 3.573A pdb=" N TRP Y 623 " --> pdb=" O LEU Y 619 " (cutoff:3.500A) Processing helix chain 'Y' and resid 627 through 636 Processing helix chain 'Y' and resid 637 through 654 removed outlier: 3.928A pdb=" N ILE Y 641 " --> pdb=" O ASN Y 637 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU Y 648 " --> pdb=" O GLY Y 644 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER Y 649 " --> pdb=" O LEU Y 645 " (cutoff:3.500A) Processing helix chain 'Z' and resid 529 through 540 removed outlier: 4.150A pdb=" N MET Z 535 " --> pdb=" O GLY Z 531 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR Z 536 " --> pdb=" O ALA Z 532 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL Z 539 " --> pdb=" O MET Z 535 " (cutoff:3.500A) Processing helix chain 'Z' and resid 564 through 596 Processing helix chain 'Z' and resid 618 through 625 removed outlier: 3.604A pdb=" N ILE Z 622 " --> pdb=" O ASN Z 618 " (cutoff:3.500A) Processing helix chain 'Z' and resid 630 through 635 removed outlier: 3.511A pdb=" N GLU Z 634 " --> pdb=" O GLN Z 630 " (cutoff:3.500A) Processing helix chain 'Z' and resid 638 through 660 removed outlier: 3.826A pdb=" N TYR Z 643 " --> pdb=" O THR Z 639 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 496 through 497 removed outlier: 4.414A pdb=" N VAL A 36 " --> pdb=" O THR X 606 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR X 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.550A pdb=" N THR A 244 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 removed outlier: 4.291A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N CYS A 239 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 159 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 307 removed outlier: 6.668A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 317 through 323 current: chain 'A' and resid 381 through 385 removed outlier: 4.756A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 414 through 421 current: chain 'A' and resid 468 through 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 359 through 361 Processing sheet with id=AB1, first strand: chain 'B' and resid 495 through 499 removed outlier: 5.306A pdb=" N VAL Y 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL B 38 " --> pdb=" O THR Y 606 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR Y 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.701A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 94 removed outlier: 4.143A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS B 239 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE B 93 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 131 through 133 removed outlier: 3.611A pdb=" N ASN B 156 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS B 155 " --> pdb=" O PHE B 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB6, first strand: chain 'B' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 261 current: chain 'B' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 284 through 287 current: chain 'B' and resid 394 through 395 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 394 through 395 current: chain 'B' and resid 465 through 470 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 294 through 297 removed outlier: 4.063A pdb=" N HIS B 330 " --> pdb=" O THR B 297 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 374 through 378 Processing sheet with id=AB9, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.534A pdb=" N ALA C 497 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.814A pdb=" N LYS C 490 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC4, first strand: chain 'C' and resid 181 through 182 removed outlier: 3.597A pdb=" N ARG C 192 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.594A pdb=" N GLN C 287 " --> pdb=" O MET C 271 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 331 through 332 removed outlier: 7.327A pdb=" N ARG C 298 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N CYS C 445 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN C 300 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE C 443 " --> pdb=" O ASN C 300 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 376 through 378 removed outlier: 3.585A pdb=" N ARG C 419 " --> pdb=" O TYR C 384 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.518A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.501A pdb=" N VAL H 95 " --> pdb=" O SER H 33 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL H 56 " --> pdb=" O VAL H 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.596A pdb=" N VAL I 5 " --> pdb=" O LYS I 23 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 10 through 12 current: chain 'I' and resid 45 through 52 removed outlier: 3.598A pdb=" N VAL I 56 " --> pdb=" O VAL I 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 56 through 59 current: chain 'I' and resid 100E through 103 Processing sheet with id=AD3, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AD4, first strand: chain 'J' and resid 9 through 13 Processing sheet with id=AD5, first strand: chain 'J' and resid 44 through 48 removed outlier: 6.832A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE J 32 " --> pdb=" O TYR J 91 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL J 97 " --> pdb=" O SER J 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 3 through 5 removed outlier: 4.185A pdb=" N ALA L 3 " --> pdb=" O SER L 26 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.829A pdb=" N THR L 105 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.519A pdb=" N VAL P 5 " --> pdb=" O LYS P 23 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET P 80 " --> pdb=" O VAL P 20 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR P 68 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 10 through 11 current: chain 'P' and resid 45 through 51 removed outlier: 4.065A pdb=" N VAL P 50 " --> pdb=" O ASN P 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 59 current: chain 'P' and resid 100E through 103 Processing sheet with id=AE1, first strand: chain 'Q' and resid 9 through 12 removed outlier: 3.558A pdb=" N THR Q 105 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER Q 84 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 19 through 23 Processing sheet with id=AE3, first strand: chain 'Q' and resid 89 through 92 526 hydrogen bonds defined for protein. 1368 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: 5.57 Time building geometry restraints manager: 7.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5686 1.34 - 1.46: 4246 1.46 - 1.58: 8045 1.58 - 1.70: 0 1.70 - 1.82: 153 Bond restraints: 18130 Sorted by residual: bond pdb=" N GLY Q 27 " pdb=" CA GLY Q 27 " ideal model delta sigma weight residual 1.444 1.476 -0.032 9.60e-03 1.09e+04 1.10e+01 bond pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.10e+00 bond pdb=" N ILE Q 21 " pdb=" CA ILE Q 21 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.40e+00 bond pdb=" N VAL C 371 " pdb=" CA VAL C 371 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.07e+00 bond pdb=" N GLY C 263 " pdb=" CA GLY C 263 " ideal model delta sigma weight residual 1.447 1.476 -0.029 1.03e-02 9.43e+03 8.02e+00 ... (remaining 18125 not shown) Histogram of bond angle deviations from ideal: 97.60 - 104.90: 284 104.90 - 112.21: 9474 112.21 - 119.52: 5704 119.52 - 126.82: 8871 126.82 - 134.13: 291 Bond angle restraints: 24624 Sorted by residual: angle pdb=" C VAL C 446 " pdb=" N SER C 447 " pdb=" CA SER C 447 " ideal model delta sigma weight residual 122.17 115.69 6.48 1.54e+00 4.22e-01 1.77e+01 angle pdb=" N GLY Q 25 " pdb=" CA GLY Q 25 " pdb=" C GLY Q 25 " ideal model delta sigma weight residual 115.36 109.98 5.38 1.33e+00 5.65e-01 1.63e+01 angle pdb=" N THR C 387 " pdb=" CA THR C 387 " pdb=" C THR C 387 " ideal model delta sigma weight residual 113.02 108.35 4.67 1.20e+00 6.94e-01 1.51e+01 angle pdb=" N CYS C 196 " pdb=" CA CYS C 196 " pdb=" C CYS C 196 " ideal model delta sigma weight residual 113.43 108.61 4.82 1.26e+00 6.30e-01 1.46e+01 angle pdb=" CA THR A 63 " pdb=" C THR A 63 " pdb=" O THR A 63 " ideal model delta sigma weight residual 122.64 118.14 4.50 1.25e+00 6.40e-01 1.29e+01 ... (remaining 24619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 10267 21.62 - 43.24: 605 43.24 - 64.86: 93 64.86 - 86.49: 44 86.49 - 108.11: 18 Dihedral angle restraints: 11027 sinusoidal: 4495 harmonic: 6532 Sorted by residual: dihedral pdb=" CB CYS C 228 " pdb=" SG CYS C 228 " pdb=" SG CYS C 239 " pdb=" CB CYS C 239 " ideal model delta sinusoidal sigma weight residual -86.00 -173.81 87.81 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual 93.00 158.90 -65.90 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 148.27 -55.27 1 1.00e+01 1.00e-02 4.13e+01 ... (remaining 11024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 2831 0.153 - 0.307: 25 0.307 - 0.460: 2 0.460 - 0.614: 0 0.614 - 0.767: 1 Chirality restraints: 2859 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.60e+01 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.64e+01 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.72e+01 ... (remaining 2856 not shown) Planarity restraints: 3105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 262 " -0.028 2.00e-02 2.50e+03 3.54e-01 1.57e+03 pdb=" CG ASN A 262 " -0.101 2.00e-02 2.50e+03 pdb=" OD1 ASN A 262 " 0.337 2.00e-02 2.50e+03 pdb=" ND2 ASN A 262 " -0.595 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.387 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.346 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG A 601 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.122 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 601 " -0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG B 601 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B 601 " -0.075 2.00e-02 2.50e+03 pdb=" N2 NAG B 601 " 0.522 2.00e-02 2.50e+03 pdb=" O7 NAG B 601 " -0.186 2.00e-02 2.50e+03 ... (remaining 3102 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 481 2.67 - 3.23: 18016 3.23 - 3.79: 26920 3.79 - 4.34: 35728 4.34 - 4.90: 57054 Nonbonded interactions: 138199 Sorted by model distance: nonbonded pdb=" NE2 GLN L 38 " pdb=" O MET L 42 " model vdw 2.118 2.520 nonbonded pdb=" OG SER A 364 " pdb=" O THR A 372 " model vdw 2.165 2.440 nonbonded pdb=" O LEU B 369 " pdb=" OG1 THR B 373 " model vdw 2.173 2.440 nonbonded pdb=" OG SER L 12 " pdb=" OG1 THR L 105 " model vdw 2.188 2.440 nonbonded pdb=" O PRO J 7 " pdb=" OG1 THR J 102 " model vdw 2.190 2.440 ... (remaining 138194 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 34 and (name N or name CA or name C or name O or name CB \ )) or resid 35 through 56 or (resid 57 through 58 and (name N or name CA or name \ C or name O or name CB )) or resid 63 or (resid 72 through 73 and (name N or na \ me CA or name C or name O or name CB )) or resid 75 through 113 or resid 119 or \ (resid 120 through 121 and (name N or name CA or name C or name O or name CB )) \ or resid 122 or (resid 123 and (name N or name CA or name C or name O or name CB \ )) or resid 124 or (resid 125 through 126 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 130 through 131 and (name N or name CA or name C o \ r name O or name CB )) or resid 132 through 138 or (resid 151 through 153 and (n \ ame N or name CA or name C or name O or name CB )) or resid 154 through 162 or r \ esid 172 through 207 or resid 210 or (resid 211 and (name N or name CA or name C \ or name O or name CB )) or resid 212 through 231 or (resid 232 and (name N or n \ ame CA or name C or name O or name CB )) or resid 233 through 306 or resid 315 t \ hrough 352 or resid 356 through 391 or (resid 392 and (name N or name CA or name \ C or name O or name CB )) or resid 393 through 396 or resid 415 through 420 or \ (resid 421 and (name N or name CA or name C or name O or name CB )) or resid 422 \ through 457 or resid 467 through 483 or (resid 484 through 485 and (name N or n \ ame CA or name C or name O or name CB )) or resid 486 through 499 or (resid 500 \ through 503 and (name N or name CA or name C or name O or name CB )) or resid 60 \ 1)) selection = (chain 'B' and (resid 34 through 45 or (resid 46 through 51 and (name N or name \ CA or name C or name O or name CB )) or resid 52 through 56 or (resid 57 through \ 58 and (name N or name CA or name C or name O or name CB )) or (resid 63 and (n \ ame N or name CA or name C or name O or name CB )) or resid 72 through 77 or (re \ sid 78 and (name N or name CA or name C or name O or name CB )) or resid 79 thro \ ugh 119 or (resid 120 through 121 and (name N or name CA or name C or name O or \ name CB )) or resid 122 or (resid 123 and (name N or name CA or name C or name O \ or name CB )) or resid 124 or (resid 125 through 131 and (name N or name CA or \ name C or name O or name CB )) or resid 132 through 194 or (resid 195 and (name \ N or name CA or name C or name O or name CB )) or resid 196 through 231 or (resi \ d 232 and (name N or name CA or name C or name O or name CB )) or resid 233 thro \ ugh 267 or resid 270 through 306 or resid 315 through 324 or resid 326 through 3 \ 52 or resid 356 through 391 or (resid 392 and (name N or name CA or name C or na \ me O or name CB )) or resid 393 through 396 or resid 415 through 420 or (resid 4 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 422 through \ 457 or resid 467 through 483 or (resid 484 through 485 and (name N or name CA o \ r name C or name O or name CB )) or resid 486 through 503 or resid 602)) selection = (chain 'C' and ((resid 34 and (name N or name CA or name C or name O or name CB \ )) or resid 35 through 45 or (resid 46 through 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 58 or (resid 71 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 75 through 113 or re \ sid 119 through 125 or (resid 126 and (name N or name CA or name C or name O or \ name CB )) or (resid 130 through 131 and (name N or name CA or name C or name O \ or name CB )) or resid 132 through 138 or (resid 151 through 153 and (name N or \ name CA or name C or name O or name CB )) or resid 154 through 162 or resid 172 \ through 194 or (resid 195 and (name N or name CA or name C or name O or name CB \ )) or resid 196 through 207 or resid 210 or (resid 211 and (name N or name CA or \ name C or name O or name CB )) or resid 212 through 267 or resid 270 through 30 \ 6 or resid 315 through 324 or resid 326 through 499 or (resid 500 through 503 an \ d (name N or name CA or name C or name O or name CB )) or resid 601)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'K' } ncs_group { reference = (chain 'H' and (resid 2 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 63 or (resid 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 71 or (resid 72 and (n \ ame N or name CA or name C or name O or name CB )) or resid 73 or resid 76 throu \ gh 96 or (resid 97 through 98 and (name N or name CA or name C or name O or name \ CB )) or resid 99 through 111)) selection = (chain 'I' and (resid 2 through 63 or (resid 64 and (name N or name CA or name C \ or name O or name CB )) or resid 65 through 71 or (resid 72 and (name N or name \ CA or name C or name O or name CB )) or resid 73 or resid 76 through 111)) selection = (chain 'P' and (resid 2 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 96 or (resid 97 through 98 and (nam \ e N or name CA or name C or name O or name CB )) or resid 99 through 111)) } ncs_group { reference = (chain 'J' and (resid 2 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 94 or (resid 95 and (name N or name \ CA or name C or name O or name CB )) or resid 95A through 106)) selection = (chain 'L' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 94 or (resid 95 and (name N or name \ CA or name C or name O or name CB )) or resid 95A or (resid 95B and (name N or \ name CA or name C or name O or name CB )) or resid 96 through 106)) selection = (chain 'Q' and (resid 2 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 59 or (resid 60 and (name N or name \ CA or name C or name O or name CB )) or resid 61 through 106)) } ncs_group { reference = (chain 'X' and (resid 522 through 534 or (resid 535 through 536 and (name N or n \ ame CA or name C or name O or name CB )) or resid 537 through 540 or (resid 563 \ through 564 and (name N or name CA or name C or name O or name CB )) or resid 56 \ 5 through 570 or (resid 571 and (name N or name CA or name C or name O or name C \ B )) or resid 572 through 647 or (resid 648 and (name N or name CA or name C or \ name O or name CB )) or resid 649 through 654)) selection = (chain 'Y' and (resid 522 through 537 or (resid 538 through 539 and (name N or n \ ame CA or name C or name O or name CB )) or resid 540 or (resid 563 through 564 \ and (name N or name CA or name C or name O or name CB )) or resid 565 through 58 \ 7 or (resid 588 and (name N or name CA or name C or name O or name CB )) or resi \ d 589 through 594 or (resid 595 and (name N or name CA or name C or name O or na \ me CB )) or resid 596 through 615 or (resid 616 and (name N or name CA or name C \ or name O or name CB )) or resid 617 through 646 or (resid 647 through 648 and \ (name N or name CA or name C or name O or name CB )) or resid 649 through 654)) selection = (chain 'Z' and (resid 522 through 535 or (resid 536 and (name N or name CA or na \ me C or name O or name CB )) or resid 537 or (resid 538 through 539 and (name N \ or name CA or name C or name O or name CB )) or resid 540 or (resid 563 through \ 564 and (name N or name CA or name C or name O or name CB )) or resid 565 throug \ h 566 or (resid 567 and (name N or name CA or name C or name O or name CB )) or \ resid 568 through 570 or (resid 571 and (name N or name CA or name C or name O o \ r name CB )) or resid 572 through 587 or (resid 588 and (name N or name CA or na \ me C or name O or name CB )) or resid 589 through 594 or (resid 595 and (name N \ or name CA or name C or name O or name CB )) or resid 596 through 615 or (resid \ 616 and (name N or name CA or name C or name O or name CB )) or resid 617 throug \ h 654)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 13.420 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 47.810 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.130 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 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 : 0.006 0.069 18130 Z= 0.372 Angle : 0.736 8.752 24624 Z= 0.418 Chirality : 0.053 0.767 2859 Planarity : 0.011 0.299 3095 Dihedral : 14.987 108.107 6724 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.88 % Favored : 91.07 % Rotamer: Outliers : 0.21 % Allowed : 0.64 % Favored : 99.15 % 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: -1.50 (0.18), residues: 2195 helix: 0.18 (0.27), residues: 367 sheet: -0.44 (0.22), residues: 572 loop : -1.67 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP Z 628 HIS 0.006 0.001 HIS C 216 PHE 0.022 0.002 PHE C 288 TYR 0.020 0.002 TYR C 217 ARG 0.004 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 293 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 VAL cc_start: 0.8279 (t) cc_final: 0.7792 (t) REVERT: B 69 TRP cc_start: 0.5838 (p-90) cc_final: 0.4313 (m100) REVERT: B 216 HIS cc_start: 0.5961 (m170) cc_final: 0.5738 (m170) REVERT: B 352 HIS cc_start: 0.7707 (t-90) cc_final: 0.7302 (t70) REVERT: C 260 LEU cc_start: 0.8548 (mp) cc_final: 0.8347 (mp) REVERT: H 10 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8245 (mp0) REVERT: H 105 ARG cc_start: 0.8026 (mmm160) cc_final: 0.7083 (mtm-85) REVERT: I 28 THR cc_start: 0.6013 (p) cc_final: 0.5435 (p) REVERT: I 80 MET cc_start: 0.3141 (ptt) cc_final: 0.2861 (ptt) REVERT: J 42 MET cc_start: 0.7653 (mpp) cc_final: 0.7419 (ttp) REVERT: J 45 LYS cc_start: 0.7825 (tptp) cc_final: 0.7510 (mttp) REVERT: P 62 LYS cc_start: 0.8187 (pptt) cc_final: 0.7065 (ptpt) REVERT: Q 39 VAL cc_start: 0.8657 (t) cc_final: 0.8278 (t) REVERT: X 535 MET cc_start: 0.8413 (mpp) cc_final: 0.8155 (mpp) REVERT: Y 584 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7954 (mt-10) REVERT: Y 618 ASN cc_start: 0.6576 (t0) cc_final: 0.6347 (m110) REVERT: Y 620 SER cc_start: 0.7095 (m) cc_final: 0.6698 (p) REVERT: Y 633 LYS cc_start: 0.8310 (mppt) cc_final: 0.7749 (mtpt) REVERT: Z 622 ILE cc_start: 0.8647 (mt) cc_final: 0.8445 (mt) outliers start: 4 outliers final: 0 residues processed: 296 average time/residue: 0.3025 time to fit residues: 134.2770 Evaluate side-chains 139 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 203 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN B 105 HIS ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN B 422 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 289 ASN Q 37 GLN Q 38 GLN Y 543 ASN ** Z 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18130 Z= 0.216 Angle : 0.616 11.024 24624 Z= 0.318 Chirality : 0.045 0.185 2859 Planarity : 0.004 0.067 3095 Dihedral : 9.469 75.813 2847 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.56 % Favored : 93.39 % Rotamer: Outliers : 0.32 % Allowed : 4.45 % Favored : 95.23 % 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: -1.14 (0.18), residues: 2195 helix: 0.81 (0.26), residues: 387 sheet: -0.20 (0.21), residues: 586 loop : -1.60 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 479 HIS 0.007 0.001 HIS B 105 PHE 0.021 0.002 PHE I 99 TYR 0.019 0.001 TYR C 191 ARG 0.004 0.000 ARG Y 542 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 213 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8696 (tpp) cc_final: 0.8464 (tpp) REVERT: B 69 TRP cc_start: 0.5908 (p-90) cc_final: 0.4332 (m100) REVERT: B 248 THR cc_start: 0.7678 (p) cc_final: 0.7468 (p) REVERT: C 203 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7195 (pt0) REVERT: H 105 ARG cc_start: 0.7965 (mmm160) cc_final: 0.7072 (mtm-85) REVERT: I 28 THR cc_start: 0.6099 (p) cc_final: 0.5295 (p) REVERT: I 29 PHE cc_start: 0.3799 (m-10) cc_final: 0.3579 (m-10) REVERT: J 45 LYS cc_start: 0.7836 (tptp) cc_final: 0.7412 (pttt) REVERT: P 62 LYS cc_start: 0.8082 (pptt) cc_final: 0.7082 (ptpt) REVERT: Q 39 VAL cc_start: 0.8515 (t) cc_final: 0.7999 (t) REVERT: Q 104 LEU cc_start: 0.8614 (tp) cc_final: 0.8274 (tp) REVERT: X 535 MET cc_start: 0.8339 (mpp) cc_final: 0.8048 (mpp) REVERT: Y 573 ILE cc_start: 0.8959 (mm) cc_final: 0.7822 (mm) REVERT: Y 620 SER cc_start: 0.7005 (m) cc_final: 0.6639 (p) REVERT: Y 633 LYS cc_start: 0.8351 (mppt) cc_final: 0.7969 (mtpt) outliers start: 6 outliers final: 0 residues processed: 218 average time/residue: 0.2829 time to fit residues: 96.9093 Evaluate side-chains 133 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 169 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 203 optimal weight: 0.0670 chunk 220 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 overall best weight: 3.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN Q 89 GLN X 563 GLN X 611 ASN ** Z 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 18130 Z= 0.371 Angle : 0.715 10.198 24624 Z= 0.369 Chirality : 0.048 0.263 2859 Planarity : 0.005 0.087 3095 Dihedral : 7.312 58.257 2847 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.66 % Favored : 91.25 % Rotamer: Outliers : 0.27 % Allowed : 6.31 % Favored : 93.43 % 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: -1.43 (0.17), residues: 2195 helix: 0.50 (0.26), residues: 386 sheet: -0.35 (0.21), residues: 591 loop : -1.80 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 35 HIS 0.023 0.002 HIS B 374 PHE 0.047 0.003 PHE P 99 TYR 0.019 0.002 TYR L 95B ARG 0.009 0.001 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 186 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8738 (tpp) cc_final: 0.8488 (tpp) REVERT: B 69 TRP cc_start: 0.5979 (p-90) cc_final: 0.4240 (m100) REVERT: B 390 LEU cc_start: 0.7833 (mt) cc_final: 0.7439 (mt) REVERT: C 203 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7252 (pt0) REVERT: H 105 ARG cc_start: 0.8286 (mmm160) cc_final: 0.6971 (mtm-85) REVERT: P 62 LYS cc_start: 0.8313 (pptt) cc_final: 0.7406 (ptpt) REVERT: Q 79 GLN cc_start: 0.8323 (mp10) cc_final: 0.8072 (mp10) REVERT: Q 104 LEU cc_start: 0.8745 (tp) cc_final: 0.8510 (tp) REVERT: X 535 MET cc_start: 0.8380 (mpp) cc_final: 0.8040 (mpp) REVERT: X 611 ASN cc_start: 0.7125 (OUTLIER) cc_final: 0.4711 (p0) REVERT: Y 620 SER cc_start: 0.7274 (m) cc_final: 0.6798 (p) REVERT: Y 633 LYS cc_start: 0.8370 (mppt) cc_final: 0.8090 (mtpt) REVERT: Z 589 ASP cc_start: 0.8471 (m-30) cc_final: 0.8108 (m-30) outliers start: 5 outliers final: 0 residues processed: 191 average time/residue: 0.2871 time to fit residues: 88.3991 Evaluate side-chains 129 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 136 optimal weight: 0.1980 chunk 204 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 315 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN B 332 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Z 607 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18130 Z= 0.188 Angle : 0.579 9.875 24624 Z= 0.296 Chirality : 0.045 0.272 2859 Planarity : 0.004 0.049 3095 Dihedral : 6.329 56.716 2847 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.01 % Favored : 93.94 % Rotamer: Outliers : 0.11 % Allowed : 3.87 % Favored : 96.02 % 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: -1.16 (0.18), residues: 2195 helix: 1.00 (0.27), residues: 380 sheet: -0.34 (0.21), residues: 605 loop : -1.63 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Z 628 HIS 0.005 0.001 HIS B 216 PHE 0.024 0.002 PHE Q 98 TYR 0.016 0.001 TYR J 87 ARG 0.007 0.000 ARG X 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.5992 (p-90) cc_final: 0.4232 (m100) REVERT: H 105 ARG cc_start: 0.8239 (mmm160) cc_final: 0.7030 (mtm-85) REVERT: L 47 LEU cc_start: 0.9189 (tp) cc_final: 0.8978 (tp) REVERT: L 48 ILE cc_start: 0.9604 (tt) cc_final: 0.9319 (pt) REVERT: Q 79 GLN cc_start: 0.8237 (mp10) cc_final: 0.7925 (mp10) REVERT: Q 104 LEU cc_start: 0.8731 (tp) cc_final: 0.8530 (tp) REVERT: X 535 MET cc_start: 0.8262 (mpp) cc_final: 0.7959 (mpp) REVERT: Z 589 ASP cc_start: 0.8441 (m-30) cc_final: 0.8049 (m-30) outliers start: 2 outliers final: 1 residues processed: 194 average time/residue: 0.2673 time to fit residues: 83.2937 Evaluate side-chains 127 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 184 optimal weight: 0.0060 chunk 149 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18130 Z= 0.175 Angle : 0.554 9.626 24624 Z= 0.286 Chirality : 0.044 0.251 2859 Planarity : 0.004 0.064 3095 Dihedral : 5.962 57.693 2847 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.47 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: -1.04 (0.18), residues: 2195 helix: 1.13 (0.27), residues: 382 sheet: -0.22 (0.21), residues: 599 loop : -1.59 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP X 571 HIS 0.004 0.001 HIS A 249 PHE 0.022 0.001 PHE C 288 TYR 0.018 0.001 TYR L 87 ARG 0.004 0.000 ARG B 350 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8144 (t0) cc_final: 0.7878 (t0) REVERT: B 69 TRP cc_start: 0.5910 (p-90) cc_final: 0.4185 (m100) REVERT: C 475 MET cc_start: 0.8606 (mmm) cc_final: 0.8204 (mmm) REVERT: H 105 ARG cc_start: 0.7899 (mmm160) cc_final: 0.6692 (mtm-85) REVERT: L 47 LEU cc_start: 0.9182 (tp) cc_final: 0.8933 (tp) REVERT: L 48 ILE cc_start: 0.9608 (tt) cc_final: 0.9326 (pt) REVERT: P 62 LYS cc_start: 0.8121 (pptt) cc_final: 0.6979 (ptpt) REVERT: Q 79 GLN cc_start: 0.8202 (mp10) cc_final: 0.7877 (mp10) REVERT: Q 104 LEU cc_start: 0.8785 (tp) cc_final: 0.8567 (tp) REVERT: X 535 MET cc_start: 0.8306 (mpp) cc_final: 0.8011 (mpp) REVERT: Z 589 ASP cc_start: 0.8480 (m-30) cc_final: 0.8099 (m-30) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2451 time to fit residues: 78.3668 Evaluate side-chains 140 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN Q 89 GLN ** Z 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18130 Z= 0.334 Angle : 0.661 10.005 24624 Z= 0.342 Chirality : 0.046 0.266 2859 Planarity : 0.005 0.081 3095 Dihedral : 6.283 56.376 2847 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.29 % Favored : 91.66 % Rotamer: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.82 % 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: -1.36 (0.18), residues: 2195 helix: 0.70 (0.27), residues: 386 sheet: -0.43 (0.21), residues: 605 loop : -1.75 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP Z 628 HIS 0.010 0.002 HIS A 330 PHE 0.019 0.002 PHE I 27 TYR 0.029 0.002 TYR L 87 ARG 0.009 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6035 (p-90) cc_final: 0.4186 (m100) REVERT: B 192 ARG cc_start: 0.4767 (ptt180) cc_final: 0.3615 (tpt170) REVERT: I 100 MET cc_start: 0.6481 (ppp) cc_final: 0.5732 (ppp) REVERT: Q 60 ASP cc_start: 0.7890 (t0) cc_final: 0.7675 (t0) REVERT: Q 79 GLN cc_start: 0.8282 (mp10) cc_final: 0.7988 (mp10) REVERT: X 535 MET cc_start: 0.8290 (mpp) cc_final: 0.7912 (mpp) REVERT: Z 589 ASP cc_start: 0.8453 (m-30) cc_final: 0.8130 (m-30) outliers start: 1 outliers final: 1 residues processed: 172 average time/residue: 0.2562 time to fit residues: 70.7758 Evaluate side-chains 114 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 158 optimal weight: 0.0980 chunk 122 optimal weight: 0.5980 chunk 182 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18130 Z= 0.160 Angle : 0.561 9.582 24624 Z= 0.288 Chirality : 0.044 0.257 2859 Planarity : 0.004 0.051 3095 Dihedral : 5.733 55.644 2847 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.69 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: -1.17 (0.18), residues: 2195 helix: 0.91 (0.27), residues: 386 sheet: -0.41 (0.21), residues: 639 loop : -1.60 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 45 HIS 0.007 0.001 HIS B 216 PHE 0.021 0.001 PHE C 317 TYR 0.016 0.001 TYR J 87 ARG 0.005 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6070 (p-90) cc_final: 0.4237 (m100) REVERT: B 192 ARG cc_start: 0.4578 (ptt180) cc_final: 0.3335 (tpt170) REVERT: B 483 LEU cc_start: 0.8025 (mm) cc_final: 0.7771 (mp) REVERT: I 80 MET cc_start: 0.3385 (ptt) cc_final: 0.3167 (ptt) REVERT: I 86 ASP cc_start: 0.5533 (m-30) cc_final: 0.5306 (m-30) REVERT: L 47 LEU cc_start: 0.9079 (tp) cc_final: 0.8868 (tp) REVERT: L 48 ILE cc_start: 0.9591 (tt) cc_final: 0.9335 (pt) REVERT: Q 60 ASP cc_start: 0.7842 (t0) cc_final: 0.7598 (t0) REVERT: Q 76 THR cc_start: 0.8652 (m) cc_final: 0.8336 (p) REVERT: Q 79 GLN cc_start: 0.8154 (mp10) cc_final: 0.7883 (mp10) REVERT: X 535 MET cc_start: 0.8247 (mpp) cc_final: 0.7915 (mpp) REVERT: Z 589 ASP cc_start: 0.8446 (m-30) cc_final: 0.8103 (m-30) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2504 time to fit residues: 74.5478 Evaluate side-chains 135 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 GLN ** Z 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 18130 Z= 0.321 Angle : 0.638 9.853 24624 Z= 0.328 Chirality : 0.046 0.314 2859 Planarity : 0.005 0.049 3095 Dihedral : 5.999 57.387 2847 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.29 % Favored : 91.66 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: -1.33 (0.18), residues: 2195 helix: 0.85 (0.27), residues: 380 sheet: -0.44 (0.21), residues: 623 loop : -1.76 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP Z 571 HIS 0.008 0.001 HIS A 330 PHE 0.035 0.002 PHE P 99 TYR 0.018 0.002 TYR L 95B ARG 0.008 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6111 (p-90) cc_final: 0.4125 (m100) REVERT: H 53 LEU cc_start: 0.7119 (tt) cc_final: 0.6918 (tp) REVERT: I 86 ASP cc_start: 0.5633 (m-30) cc_final: 0.5339 (m-30) REVERT: P 62 LYS cc_start: 0.8274 (pptt) cc_final: 0.7160 (ptpt) REVERT: Q 60 ASP cc_start: 0.7989 (t0) cc_final: 0.7731 (t0) REVERT: X 535 MET cc_start: 0.8275 (mpp) cc_final: 0.7878 (mpp) REVERT: Z 589 ASP cc_start: 0.8492 (m-30) cc_final: 0.8179 (m-30) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2621 time to fit residues: 69.2745 Evaluate side-chains 120 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.9980 chunk 206 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 chunk 201 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 GLN ** Z 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18130 Z= 0.210 Angle : 0.594 13.887 24624 Z= 0.305 Chirality : 0.046 0.290 2859 Planarity : 0.004 0.050 3095 Dihedral : 5.844 56.143 2847 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.33 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.27 (0.18), residues: 2195 helix: 0.85 (0.27), residues: 386 sheet: -0.40 (0.21), residues: 625 loop : -1.72 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP Z 571 HIS 0.009 0.001 HIS B 216 PHE 0.023 0.001 PHE C 288 TYR 0.014 0.001 TYR C 191 ARG 0.006 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6088 (p-90) cc_final: 0.4121 (m100) REVERT: B 216 HIS cc_start: 0.7313 (m170) cc_final: 0.7106 (m170) REVERT: B 483 LEU cc_start: 0.8030 (mm) cc_final: 0.7729 (mp) REVERT: H 53 LEU cc_start: 0.7061 (tt) cc_final: 0.6631 (tp) REVERT: I 86 ASP cc_start: 0.5640 (m-30) cc_final: 0.5295 (m-30) REVERT: P 62 LYS cc_start: 0.8215 (pptt) cc_final: 0.7105 (ptpt) REVERT: Q 60 ASP cc_start: 0.7991 (t0) cc_final: 0.7718 (t0) REVERT: X 535 MET cc_start: 0.8246 (mpp) cc_final: 0.7882 (mpp) REVERT: Z 571 TRP cc_start: 0.8053 (m-10) cc_final: 0.7810 (m100) REVERT: Z 589 ASP cc_start: 0.8463 (m-30) cc_final: 0.8110 (m-30) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2457 time to fit residues: 68.3474 Evaluate side-chains 125 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 129 optimal weight: 0.0070 chunk 100 optimal weight: 2.9990 chunk 147 optimal weight: 0.0050 chunk 223 optimal weight: 5.9990 chunk 205 optimal weight: 0.5980 chunk 177 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.9216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18130 Z= 0.183 Angle : 0.571 9.555 24624 Z= 0.292 Chirality : 0.045 0.272 2859 Planarity : 0.004 0.051 3095 Dihedral : 5.625 56.619 2847 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.97 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.13 (0.18), residues: 2195 helix: 1.05 (0.27), residues: 381 sheet: -0.30 (0.21), residues: 625 loop : -1.66 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP Z 571 HIS 0.009 0.001 HIS B 216 PHE 0.021 0.001 PHE C 288 TYR 0.015 0.001 TYR C 191 ARG 0.005 0.000 ARG H 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.6052 (p-90) cc_final: 0.4139 (m100) REVERT: B 483 LEU cc_start: 0.7987 (mm) cc_final: 0.7778 (mp) REVERT: H 53 LEU cc_start: 0.7036 (tt) cc_final: 0.6590 (tp) REVERT: I 86 ASP cc_start: 0.5590 (m-30) cc_final: 0.5314 (m-30) REVERT: J 85 ASP cc_start: 0.7108 (t0) cc_final: 0.6843 (t0) REVERT: Q 60 ASP cc_start: 0.7995 (t0) cc_final: 0.7705 (t0) REVERT: Q 76 THR cc_start: 0.8420 (m) cc_final: 0.8140 (p) REVERT: X 535 MET cc_start: 0.8203 (mpp) cc_final: 0.7839 (mpp) REVERT: Z 571 TRP cc_start: 0.7906 (m-10) cc_final: 0.7685 (m100) REVERT: Z 589 ASP cc_start: 0.8492 (m-30) cc_final: 0.8102 (m-30) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2630 time to fit residues: 74.4106 Evaluate side-chains 129 residues out of total 1982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 8.9990 chunk 189 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 163 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 182 optimal weight: 0.0060 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 GLN ** Z 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.079580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.066903 restraints weight = 75372.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.066683 restraints weight = 67761.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.066976 restraints weight = 59809.152| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 18130 Z= 0.340 Angle : 0.666 9.855 24624 Z= 0.343 Chirality : 0.048 0.273 2859 Planarity : 0.005 0.055 3095 Dihedral : 6.073 57.466 2847 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.07 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.41 (0.18), residues: 2195 helix: 0.74 (0.27), residues: 383 sheet: -0.45 (0.21), residues: 623 loop : -1.83 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP Z 571 HIS 0.009 0.002 HIS A 330 PHE 0.036 0.002 PHE P 99 TYR 0.019 0.002 TYR L 87 ARG 0.007 0.001 ARG H 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3050.30 seconds wall clock time: 56 minutes 47.15 seconds (3407.15 seconds total)