Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 14:15:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6np0_0469/07_2023/6np0_0469_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6np0_0469/07_2023/6np0_0469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6np0_0469/07_2023/6np0_0469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6np0_0469/07_2023/6np0_0469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6np0_0469/07_2023/6np0_0469_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6np0_0469/07_2023/6np0_0469_neut_updated.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 Cl 1 4.86 5 C 11095 2.51 5 N 2720 2.21 5 O 3025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 400": "NH1" <-> "NH2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C ARG 410": "NH1" <-> "NH2" Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D ARG 410": "NH1" <-> "NH2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 328": "NH1" <-> "NH2" Residue "E ARG 400": "NH1" <-> "NH2" Residue "E ARG 410": "NH1" <-> "NH2" Residue "E ARG 420": "NH1" <-> "NH2" Residue "E ARG 439": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 16891 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3260 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3260 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3260 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3260 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3260 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 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 chiralities: 3 Chain: "G" 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 chiralities: 2 Chain: "H" 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 chiralities: 3 Chain: "I" 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 chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" 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 chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" 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 chiralities: 3 Chain: "O" 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 chiralities: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {' CL': 1, 'CWB': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'CWB': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'CWB': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 74 Unusual residues: {'CWB': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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 chiralities: 2 Time building chain proxies: 8.26, per 1000 atoms: 0.49 Number of scatterers: 16891 At special positions: 0 Unit cell: (104.272, 106.4, 173.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 50 16.00 O 3025 8.00 N 2720 7.00 C 11095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=5, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG G 1 " - " ASN A 148 " " NAG I 1 " - " ASN B 148 " " NAG K 1 " - " ASN C 148 " " NAG M 1 " - " ASN D 148 " " NAG O 1 " - " ASN E 148 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.50 Conformation dependent library (CDL) restraints added in 2.2 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 20 sheets defined 38.0% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 14 through 19 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 228 through 243 removed outlier: 3.834A pdb=" N MET A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 250 through 270 removed outlier: 3.622A pdb=" N ILE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 307 removed outlier: 3.514A pdb=" N ILE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 331 No H-bonds generated for 'chain 'A' and resid 328 through 331' Processing helix chain 'A' and resid 398 through 460 removed outlier: 3.706A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 415 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 423 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 19 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 228 through 243 removed outlier: 3.834A pdb=" N MET B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 250 through 270 removed outlier: 3.622A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 307 removed outlier: 3.513A pdb=" N ILE B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 331 No H-bonds generated for 'chain 'B' and resid 328 through 331' Processing helix chain 'B' and resid 398 through 460 removed outlier: 3.706A pdb=" N SER B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 415 " --> pdb=" O HIS B 411 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 423 " --> pdb=" O MET B 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 228 through 243 removed outlier: 3.834A pdb=" N MET C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'C' and resid 250 through 270 removed outlier: 3.622A pdb=" N ILE C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 307 removed outlier: 3.513A pdb=" N ILE C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 331 No H-bonds generated for 'chain 'C' and resid 328 through 331' Processing helix chain 'C' and resid 398 through 460 removed outlier: 3.706A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 415 " --> pdb=" O HIS C 411 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA C 423 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 222 through 224 No H-bonds generated for 'chain 'D' and resid 222 through 224' Processing helix chain 'D' and resid 228 through 243 removed outlier: 3.835A pdb=" N MET D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 248 No H-bonds generated for 'chain 'D' and resid 246 through 248' Processing helix chain 'D' and resid 250 through 270 removed outlier: 3.622A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 307 removed outlier: 3.514A pdb=" N ILE D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 331 No H-bonds generated for 'chain 'D' and resid 328 through 331' Processing helix chain 'D' and resid 398 through 460 removed outlier: 3.706A pdb=" N SER D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 415 " --> pdb=" O HIS D 411 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG D 416 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA D 423 " --> pdb=" O MET D 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 228 through 243 removed outlier: 3.834A pdb=" N MET E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 248 No H-bonds generated for 'chain 'E' and resid 246 through 248' Processing helix chain 'E' and resid 250 through 270 removed outlier: 3.621A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 307 removed outlier: 3.514A pdb=" N ILE E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 331 No H-bonds generated for 'chain 'E' and resid 328 through 331' Processing helix chain 'E' and resid 398 through 460 removed outlier: 3.706A pdb=" N SER E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS E 415 " --> pdb=" O HIS E 411 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG E 416 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA E 423 " --> pdb=" O MET E 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE E 458 " --> pdb=" O THR E 454 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.180A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 50 through 52 Processing sheet with id= C, first strand: chain 'A' and resid 85 through 89 Processing sheet with id= D, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.241A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.179A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 50 through 52 Processing sheet with id= G, first strand: chain 'B' and resid 85 through 89 Processing sheet with id= H, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.241A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.179A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 50 through 52 Processing sheet with id= K, first strand: chain 'C' and resid 85 through 89 Processing sheet with id= L, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.241A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.179A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 50 through 52 Processing sheet with id= O, first strand: chain 'D' and resid 85 through 89 Processing sheet with id= P, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.241A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 163 through 167 removed outlier: 6.180A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 50 through 52 Processing sheet with id= S, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= T, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.241A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2115 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: 4.38 Time building geometry restraints manager: 7.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2565 1.31 - 1.43: 4947 1.43 - 1.56: 9721 1.56 - 1.68: 47 1.68 - 1.80: 75 Bond restraints: 17355 Sorted by residual: bond pdb=" C01 CWB D 509 " pdb=" N02 CWB D 509 " ideal model delta sigma weight residual 1.445 1.184 0.261 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C01 CWB B 508 " pdb=" N02 CWB B 508 " ideal model delta sigma weight residual 1.445 1.185 0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C01 CWB D 508 " pdb=" N02 CWB D 508 " ideal model delta sigma weight residual 1.445 1.186 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C01 CWB A 508 " pdb=" N02 CWB A 508 " ideal model delta sigma weight residual 1.445 1.187 0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C01 CWB C 508 " pdb=" N02 CWB C 508 " ideal model delta sigma weight residual 1.445 1.187 0.258 2.00e-02 2.50e+03 1.67e+02 ... (remaining 17350 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.66: 641 106.66 - 113.69: 9885 113.69 - 120.72: 7573 120.72 - 127.76: 5366 127.76 - 134.79: 255 Bond angle restraints: 23720 Sorted by residual: angle pdb=" C3 NAG F 1 " pdb=" C4 NAG F 1 " pdb=" O4 NAG F 1 " ideal model delta sigma weight residual 107.29 134.36 -27.07 3.00e+00 1.11e-01 8.14e+01 angle pdb=" C3 NAG N 1 " pdb=" C4 NAG N 1 " pdb=" O4 NAG N 1 " ideal model delta sigma weight residual 107.29 134.34 -27.05 3.00e+00 1.11e-01 8.13e+01 angle pdb=" C3 NAG J 1 " pdb=" C4 NAG J 1 " pdb=" O4 NAG J 1 " ideal model delta sigma weight residual 107.29 134.30 -27.01 3.00e+00 1.11e-01 8.10e+01 angle pdb=" C3 NAG L 1 " pdb=" C4 NAG L 1 " pdb=" O4 NAG L 1 " ideal model delta sigma weight residual 107.29 134.29 -27.00 3.00e+00 1.11e-01 8.10e+01 angle pdb=" C3 NAG H 1 " pdb=" C4 NAG H 1 " pdb=" O4 NAG H 1 " ideal model delta sigma weight residual 107.29 134.26 -26.97 3.00e+00 1.11e-01 8.08e+01 ... (remaining 23715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.76: 8405 9.76 - 19.52: 1035 19.52 - 29.28: 260 29.28 - 39.04: 155 39.04 - 48.81: 25 Dihedral angle restraints: 9880 sinusoidal: 3985 harmonic: 5895 Sorted by residual: dihedral pdb=" CA LEU A 12 " pdb=" C LEU A 12 " pdb=" N LEU A 13 " pdb=" CA LEU A 13 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA LEU E 12 " pdb=" C LEU E 12 " pdb=" N LEU E 13 " pdb=" CA LEU E 13 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA LEU D 12 " pdb=" C LEU D 12 " pdb=" N LEU D 13 " pdb=" CA LEU D 13 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 9877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 2769 0.170 - 0.340: 46 0.340 - 0.509: 0 0.509 - 0.679: 0 0.679 - 0.849: 10 Chirality restraints: 2825 Sorted by residual: chirality pdb=" C4 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O4 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.68 -0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" C4 NAG J 1 " pdb=" C3 NAG J 1 " pdb=" C5 NAG J 1 " pdb=" O4 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.68 -0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" C4 NAG N 1 " pdb=" C3 NAG N 1 " pdb=" C5 NAG N 1 " pdb=" O4 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.68 -0.85 2.00e-01 2.50e+01 1.79e+01 ... (remaining 2822 not shown) Planarity restraints: 2860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 168 " 0.022 2.00e-02 2.50e+03 1.95e-02 9.51e+00 pdb=" CG TRP E 168 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP E 168 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP E 168 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 168 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 168 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 168 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 168 " 0.022 2.00e-02 2.50e+03 1.94e-02 9.37e+00 pdb=" CG TRP B 168 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 168 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 168 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 168 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 168 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 168 " 0.022 2.00e-02 2.50e+03 1.93e-02 9.36e+00 pdb=" CG TRP A 168 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 168 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 168 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 168 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 168 " -0.000 2.00e-02 2.50e+03 ... (remaining 2857 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4142 2.80 - 3.32: 14682 3.32 - 3.85: 27933 3.85 - 4.37: 30758 4.37 - 4.90: 53384 Nonbonded interactions: 130899 Sorted by model distance: nonbonded pdb=" N ASP B 91 " pdb=" OD1 ASP B 91 " model vdw 2.270 2.520 nonbonded pdb=" N ASP D 91 " pdb=" OD1 ASP D 91 " model vdw 2.271 2.520 nonbonded pdb=" N ASP A 91 " pdb=" OD1 ASP A 91 " model vdw 2.271 2.520 nonbonded pdb=" N ASP C 91 " pdb=" OD1 ASP C 91 " model vdw 2.271 2.520 nonbonded pdb=" N ASP E 91 " pdb=" OD1 ASP E 91 " model vdw 2.271 2.520 ... (remaining 130894 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 7 through 462 or resid 501 through 502)) selection = (chain 'B' and (resid 7 through 462 or resid 501 through 502)) selection = (chain 'C' and (resid 7 through 462 or resid 501 through 502)) selection = (chain 'D' and (resid 7 through 462 or resid 501 through 502)) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.950 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 40.800 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 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 : 0.011 0.261 17355 Z= 0.686 Angle : 1.286 27.069 23720 Z= 0.612 Chirality : 0.079 0.849 2825 Planarity : 0.006 0.046 2855 Dihedral : 10.430 48.806 6040 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 0.55 % 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: -3.90 (0.15), residues: 1955 helix: -2.22 (0.14), residues: 805 sheet: -2.02 (0.22), residues: 405 loop : -3.15 (0.17), residues: 745 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 350 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 356 average time/residue: 1.1420 time to fit residues: 457.7309 Evaluate side-chains 162 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 157 time to evaluate : 1.949 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 2.5682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 311 GLN B 9 GLN B 184 GLN C 82 ASN C 101 ASN ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN D 111 ASN D 309 HIS E 82 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 17355 Z= 0.254 Angle : 0.773 10.947 23720 Z= 0.363 Chirality : 0.049 0.240 2825 Planarity : 0.005 0.040 2855 Dihedral : 5.130 20.900 2190 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 5.15 % 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: -2.02 (0.17), residues: 1955 helix: -0.24 (0.17), residues: 800 sheet: -1.77 (0.22), residues: 460 loop : -2.18 (0.21), residues: 695 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 189 time to evaluate : 2.118 Fit side-chains outliers start: 94 outliers final: 46 residues processed: 264 average time/residue: 0.9576 time to fit residues: 291.7996 Evaluate side-chains 193 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 147 time to evaluate : 1.999 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 39 residues processed: 8 average time/residue: 0.2414 time to fit residues: 5.6895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 177 optimal weight: 0.0570 chunk 191 optimal weight: 2.9990 chunk 157 optimal weight: 0.0020 chunk 175 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 142 optimal weight: 0.9980 overall best weight: 0.4506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS C 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 17355 Z= 0.163 Angle : 0.660 9.558 23720 Z= 0.305 Chirality : 0.045 0.173 2825 Planarity : 0.003 0.037 2855 Dihedral : 4.596 17.487 2190 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 4.38 % 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: -1.05 (0.19), residues: 1955 helix: 0.93 (0.19), residues: 800 sheet: -1.61 (0.22), residues: 460 loop : -1.89 (0.21), residues: 695 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 160 time to evaluate : 1.857 Fit side-chains outliers start: 80 outliers final: 48 residues processed: 228 average time/residue: 0.9694 time to fit residues: 255.2211 Evaluate side-chains 189 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 141 time to evaluate : 2.054 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 44 residues processed: 5 average time/residue: 0.6640 time to fit residues: 6.6399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.9980 chunk 133 optimal weight: 0.0370 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 0.0170 chunk 84 optimal weight: 0.9990 chunk 119 optimal weight: 0.0050 chunk 178 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 93 optimal weight: 0.0970 chunk 168 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.1708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 17355 Z= 0.126 Angle : 0.595 8.545 23720 Z= 0.276 Chirality : 0.044 0.168 2825 Planarity : 0.003 0.032 2855 Dihedral : 4.146 15.754 2190 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 5.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.19), residues: 1955 helix: 1.74 (0.19), residues: 775 sheet: -1.42 (0.22), residues: 460 loop : -1.63 (0.21), residues: 720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 162 time to evaluate : 2.040 Fit side-chains outliers start: 93 outliers final: 46 residues processed: 238 average time/residue: 0.9531 time to fit residues: 263.0986 Evaluate side-chains 189 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 143 time to evaluate : 1.966 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 41 residues processed: 6 average time/residue: 0.6569 time to fit residues: 7.4891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 17355 Z= 0.216 Angle : 0.671 10.577 23720 Z= 0.311 Chirality : 0.046 0.181 2825 Planarity : 0.004 0.036 2855 Dihedral : 4.308 19.353 2190 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 5.15 % 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: -0.14 (0.19), residues: 1955 helix: 1.89 (0.19), residues: 775 sheet: -1.35 (0.22), residues: 460 loop : -1.40 (0.22), residues: 720 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 160 time to evaluate : 2.100 Fit side-chains outliers start: 94 outliers final: 53 residues processed: 238 average time/residue: 0.9255 time to fit residues: 256.1440 Evaluate side-chains 186 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 133 time to evaluate : 1.859 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 49 residues processed: 6 average time/residue: 0.8845 time to fit residues: 8.6167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 188 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 17355 Z= 0.287 Angle : 0.703 10.952 23720 Z= 0.327 Chirality : 0.048 0.202 2825 Planarity : 0.004 0.040 2855 Dihedral : 4.513 18.028 2190 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 5.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.19), residues: 1955 helix: 1.79 (0.19), residues: 775 sheet: -1.35 (0.23), residues: 470 loop : -1.32 (0.23), residues: 710 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 138 time to evaluate : 2.030 Fit side-chains outliers start: 92 outliers final: 50 residues processed: 217 average time/residue: 0.9636 time to fit residues: 242.4117 Evaluate side-chains 170 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 120 time to evaluate : 1.898 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 44 residues processed: 6 average time/residue: 0.2156 time to fit residues: 4.7204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 105 optimal weight: 0.0060 chunk 187 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 17355 Z= 0.174 Angle : 0.631 9.772 23720 Z= 0.291 Chirality : 0.045 0.173 2825 Planarity : 0.003 0.032 2855 Dihedral : 4.226 16.633 2190 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 3.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1955 helix: 2.00 (0.19), residues: 775 sheet: -1.27 (0.23), residues: 470 loop : -1.19 (0.23), residues: 710 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 133 time to evaluate : 1.934 Fit side-chains outliers start: 72 outliers final: 49 residues processed: 199 average time/residue: 0.9481 time to fit residues: 219.8951 Evaluate side-chains 170 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 121 time to evaluate : 1.948 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 47 residues processed: 4 average time/residue: 0.2197 time to fit residues: 4.0662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 17355 Z= 0.175 Angle : 0.632 10.698 23720 Z= 0.290 Chirality : 0.044 0.173 2825 Planarity : 0.003 0.032 2855 Dihedral : 4.115 16.650 2190 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 4.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1955 helix: 2.08 (0.19), residues: 775 sheet: -1.22 (0.23), residues: 470 loop : -1.09 (0.23), residues: 710 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 123 time to evaluate : 2.043 Fit side-chains outliers start: 75 outliers final: 61 residues processed: 185 average time/residue: 0.9931 time to fit residues: 212.0321 Evaluate side-chains 180 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 119 time to evaluate : 1.897 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 50 residues processed: 12 average time/residue: 0.4933 time to fit residues: 10.0161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.5980 chunk 164 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 17355 Z= 0.181 Angle : 0.625 9.097 23720 Z= 0.288 Chirality : 0.045 0.172 2825 Planarity : 0.003 0.032 2855 Dihedral : 4.083 16.979 2190 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1955 helix: 2.13 (0.19), residues: 775 sheet: -1.20 (0.23), residues: 470 loop : -1.05 (0.23), residues: 710 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 128 time to evaluate : 2.130 Fit side-chains outliers start: 73 outliers final: 53 residues processed: 193 average time/residue: 1.0546 time to fit residues: 233.8715 Evaluate side-chains 174 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 121 time to evaluate : 2.009 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 49 residues processed: 4 average time/residue: 0.7390 time to fit residues: 6.1672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 0.0070 chunk 113 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 178 optimal weight: 0.4980 chunk 154 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 17355 Z= 0.149 Angle : 0.613 9.434 23720 Z= 0.281 Chirality : 0.044 0.161 2825 Planarity : 0.003 0.031 2855 Dihedral : 3.960 16.298 2190 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.20), residues: 1955 helix: 2.19 (0.19), residues: 775 sheet: -1.15 (0.24), residues: 465 loop : -0.98 (0.23), residues: 715 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 137 time to evaluate : 2.072 Fit side-chains outliers start: 58 outliers final: 51 residues processed: 185 average time/residue: 1.0084 time to fit residues: 216.3369 Evaluate side-chains 177 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 126 time to evaluate : 2.023 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 44 residues processed: 8 average time/residue: 0.9444 time to fit residues: 11.5644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 136 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.118622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.083381 restraints weight = 26748.760| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.27 r_work: 0.2915 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 17355 Z= 0.170 Angle : 0.612 9.093 23720 Z= 0.283 Chirality : 0.044 0.166 2825 Planarity : 0.003 0.031 2855 Dihedral : 3.961 16.643 2190 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 3.23 % 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: 0.36 (0.20), residues: 1955 helix: 2.22 (0.19), residues: 775 sheet: -1.13 (0.24), residues: 465 loop : -0.98 (0.24), residues: 715 =============================================================================== Job complete usr+sys time: 5186.61 seconds wall clock time: 93 minutes 30.24 seconds (5610.24 seconds total)