Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 00:24:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qfa_4542/04_2023/6qfa_4542_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qfa_4542/04_2023/6qfa_4542.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qfa_4542/04_2023/6qfa_4542_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qfa_4542/04_2023/6qfa_4542_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qfa_4542/04_2023/6qfa_4542_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qfa_4542/04_2023/6qfa_4542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qfa_4542/04_2023/6qfa_4542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qfa_4542/04_2023/6qfa_4542_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qfa_4542/04_2023/6qfa_4542_updated.pdb" } resolution = 2.49 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= 0.014 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 12130 2.51 5 N 3060 2.21 5 O 3465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 488": "NH1" <-> "NH2" Residue "O ARG 488": "NH1" <-> "NH2" Residue "N ARG 488": "NH1" <-> "NH2" Residue "M ARG 488": "NH1" <-> "NH2" Residue "L ARG 488": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18755 Number of models: 1 Model: "" Number of chains: 20 Chain: "B" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "K" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "O" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "N" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "L" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "C" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "D" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "E" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "A" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "F" 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 chiralities: 5 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 chiralities: 5 Chain: "H" 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 chiralities: 5 Chain: "I" 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 chiralities: 5 Chain: "J" 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 chiralities: 5 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.98, per 1000 atoms: 0.53 Number of scatterers: 18755 At special positions: 0 Unit cell: (143.38, 138.03, 126.26, 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 100 16.00 O 3465 8.00 N 3060 7.00 C 12130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS K 409 " - pdb=" SG CYS K 483 " distance=2.03 Simple disulfide: pdb=" SG CYS O 409 " - pdb=" SG CYS O 483 " distance=2.03 Simple disulfide: pdb=" SG CYS N 409 " - pdb=" SG CYS N 483 " distance=2.03 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 483 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " 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 F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " BETA1-4 " 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 H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 501 " - " ASN A 80 " " NAG B 501 " - " ASN B 80 " " NAG C 501 " - " ASN C 80 " " NAG D 501 " - " ASN D 80 " " NAG E 501 " - " ASN E 80 " " NAG F 1 " - " ASN B 149 " " NAG G 1 " - " ASN C 149 " " NAG H 1 " - " ASN D 149 " " NAG I 1 " - " ASN E 149 " " NAG J 1 " - " ASN A 149 " Time building additional restraints: 7.92 Conformation dependent library (CDL) restraints added in 2.8 seconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 30 sheets defined 28.4% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.581A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.687A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.549A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.841A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 305 removed outlier: 3.579A pdb=" N LEU B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 446 removed outlier: 4.108A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'K' and resid 496 through 498 No H-bonds generated for 'chain 'K' and resid 496 through 498' Processing helix chain 'O' and resid 496 through 498 No H-bonds generated for 'chain 'O' and resid 496 through 498' Processing helix chain 'N' and resid 496 through 498 No H-bonds generated for 'chain 'N' and resid 496 through 498' Processing helix chain 'M' and resid 496 through 498 No H-bonds generated for 'chain 'M' and resid 496 through 498' Processing helix chain 'L' and resid 496 through 498 No H-bonds generated for 'chain 'L' and resid 496 through 498' Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.580A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 219 through 224 removed outlier: 3.790A pdb=" N LEU C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 241 removed outlier: 3.549A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 271 removed outlier: 3.853A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 305 removed outlier: 3.579A pdb=" N LEU C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 446 removed outlier: 4.108A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.580A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 219 through 224 removed outlier: 3.687A pdb=" N LEU D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 241 removed outlier: 3.549A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 271 removed outlier: 3.582A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR D 271 " --> pdb=" O HIS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 305 removed outlier: 3.579A pdb=" N LEU D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 446 removed outlier: 4.108A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 10 through 20 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 85 through 90 removed outlier: 3.580A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 219 through 224 removed outlier: 3.687A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 241 removed outlier: 3.550A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 271 removed outlier: 3.576A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR E 271 " --> pdb=" O HIS E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 305 removed outlier: 3.579A pdb=" N LEU E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 446 removed outlier: 4.109A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.580A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.688A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.550A pdb=" N TRP A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 removed outlier: 3.587A pdb=" N GLU A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 305 removed outlier: 3.579A pdb=" N LEU A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 446 removed outlier: 4.109A pdb=" N ILE A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Proline residue: A 432 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.239A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.873A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 2 through 7 Processing sheet with id= E, first strand: chain 'K' and resid 506 through 508 removed outlier: 3.648A pdb=" N THR K 506 " --> pdb=" O TYR K 481 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL K 480 " --> pdb=" O GLN K 426 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE K 420 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG K 425 " --> pdb=" O PHE K 434 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE K 434 " --> pdb=" O ARG K 425 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 484 through 486 removed outlier: 3.897A pdb=" N TYR K 501 " --> pdb=" O ALA K 485 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'O' and resid 2 through 7 Processing sheet with id= H, first strand: chain 'O' and resid 506 through 508 removed outlier: 3.648A pdb=" N THR O 506 " --> pdb=" O TYR O 481 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL O 480 " --> pdb=" O GLN O 426 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE O 420 " --> pdb=" O LYS O 486 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG O 425 " --> pdb=" O PHE O 434 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE O 434 " --> pdb=" O ARG O 425 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'O' and resid 484 through 486 removed outlier: 3.896A pdb=" N TYR O 501 " --> pdb=" O ALA O 485 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 2 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 506 through 508 removed outlier: 3.648A pdb=" N THR N 506 " --> pdb=" O TYR N 481 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL N 480 " --> pdb=" O GLN N 426 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE N 420 " --> pdb=" O LYS N 486 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG N 425 " --> pdb=" O PHE N 434 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE N 434 " --> pdb=" O ARG N 425 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 484 through 486 removed outlier: 3.897A pdb=" N TYR N 501 " --> pdb=" O ALA N 485 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'M' and resid 2 through 7 Processing sheet with id= N, first strand: chain 'M' and resid 506 through 508 removed outlier: 3.648A pdb=" N THR M 506 " --> pdb=" O TYR M 481 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL M 480 " --> pdb=" O GLN M 426 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 484 through 486 removed outlier: 3.897A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 2 through 7 Processing sheet with id= Q, first strand: chain 'L' and resid 506 through 508 removed outlier: 3.648A pdb=" N THR L 506 " --> pdb=" O TYR L 481 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL L 480 " --> pdb=" O GLN L 426 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG L 425 " --> pdb=" O PHE L 434 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE L 434 " --> pdb=" O ARG L 425 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 484 through 486 removed outlier: 3.897A pdb=" N TYR L 501 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.274A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.851A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 164 through 168 removed outlier: 6.272A pdb=" N VAL D 36 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N TYR D 167 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL D 38 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.890A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.275A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.868A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.270A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.852A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) 792 hydrogen bonds defined for protein. 2286 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: 6.50 Time building geometry restraints manager: 8.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2983 1.32 - 1.45: 5751 1.45 - 1.57: 10336 1.57 - 1.69: 0 1.69 - 1.81: 170 Bond restraints: 19240 Sorted by residual: bond pdb=" C PRO C 34 " pdb=" O PRO C 34 " ideal model delta sigma weight residual 1.243 1.202 0.042 8.50e-03 1.38e+04 2.40e+01 bond pdb=" C PRO A 34 " pdb=" O PRO A 34 " ideal model delta sigma weight residual 1.243 1.202 0.042 8.50e-03 1.38e+04 2.40e+01 bond pdb=" C PRO B 34 " pdb=" O PRO B 34 " ideal model delta sigma weight residual 1.243 1.202 0.042 8.50e-03 1.38e+04 2.38e+01 bond pdb=" C PRO E 34 " pdb=" O PRO E 34 " ideal model delta sigma weight residual 1.243 1.202 0.041 8.50e-03 1.38e+04 2.33e+01 bond pdb=" C PRO D 34 " pdb=" O PRO D 34 " ideal model delta sigma weight residual 1.243 1.202 0.041 8.50e-03 1.38e+04 2.31e+01 ... (remaining 19235 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.27: 509 106.27 - 113.22: 10181 113.22 - 120.16: 7168 120.16 - 127.11: 8079 127.11 - 134.05: 218 Bond angle restraints: 26155 Sorted by residual: angle pdb=" C ARG C 269 " pdb=" N GLU C 270 " pdb=" CA GLU C 270 " ideal model delta sigma weight residual 120.28 125.64 -5.36 1.44e+00 4.82e-01 1.38e+01 angle pdb=" C ARG B 269 " pdb=" N GLU B 270 " pdb=" CA GLU B 270 " ideal model delta sigma weight residual 120.28 125.63 -5.35 1.44e+00 4.82e-01 1.38e+01 angle pdb=" C LEU D 223 " pdb=" N GLN D 224 " pdb=" CA GLN D 224 " ideal model delta sigma weight residual 120.29 125.01 -4.72 1.42e+00 4.96e-01 1.11e+01 angle pdb=" C LEU E 223 " pdb=" N GLN E 224 " pdb=" CA GLN E 224 " ideal model delta sigma weight residual 120.29 124.99 -4.70 1.42e+00 4.96e-01 1.10e+01 angle pdb=" N GLN B 224 " pdb=" CA GLN B 224 " pdb=" C GLN B 224 " ideal model delta sigma weight residual 111.36 114.96 -3.60 1.09e+00 8.42e-01 1.09e+01 ... (remaining 26150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 10404 17.43 - 34.86: 490 34.86 - 52.29: 66 52.29 - 69.72: 15 69.72 - 87.15: 10 Dihedral angle restraints: 10985 sinusoidal: 4340 harmonic: 6645 Sorted by residual: dihedral pdb=" CA SER E 46 " pdb=" C SER E 46 " pdb=" N ILE E 47 " pdb=" CA ILE E 47 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N ILE A 47 " pdb=" CA ILE A 47 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER B 46 " pdb=" C SER B 46 " pdb=" N ILE B 47 " pdb=" CA ILE B 47 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 10982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2317 0.059 - 0.119: 467 0.119 - 0.178: 153 0.178 - 0.237: 21 0.237 - 0.296: 7 Chirality restraints: 2965 Sorted by residual: chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.18e+02 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.14e+02 ... (remaining 2962 not shown) Planarity restraints: 3245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 227 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO B 228 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 228 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 228 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 227 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO C 228 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 228 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 228 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 227 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO A 228 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 228 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 228 " -0.031 5.00e-02 4.00e+02 ... (remaining 3242 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 136 2.56 - 3.14: 13329 3.14 - 3.73: 29316 3.73 - 4.31: 45368 4.31 - 4.90: 71708 Nonbonded interactions: 159857 Sorted by model distance: nonbonded pdb=" OD1 ASP E 101 " pdb=" OG SER E 104 " model vdw 1.973 2.440 nonbonded pdb=" OD1 ASP C 101 " pdb=" OG SER C 104 " model vdw 1.976 2.440 nonbonded pdb=" NH1 ARG E 269 " pdb=" OD1 ASP E 282 " model vdw 2.140 2.520 nonbonded pdb=" NH1 ARG D 269 " pdb=" OD1 ASP D 282 " model vdw 2.145 2.520 nonbonded pdb=" NH1 ARG A 269 " pdb=" OD1 ASP A 282 " model vdw 2.150 2.520 ... (remaining 159852 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.010 Extract box with map and model: 5.300 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 50.550 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.160 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:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 19240 Z= 0.356 Angle : 0.801 6.568 26155 Z= 0.497 Chirality : 0.058 0.296 2965 Planarity : 0.005 0.056 3235 Dihedral : 10.813 87.147 6725 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: -2.14 (0.16), residues: 2240 helix: -3.79 (0.11), residues: 615 sheet: 0.39 (0.19), residues: 670 loop : -0.92 (0.18), residues: 955 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 2.144 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 353 average time/residue: 1.3138 time to fit residues: 520.2264 Evaluate side-chains 321 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 319 time to evaluate : 1.993 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.1957 time to fit residues: 3.4972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 176 optimal weight: 0.2980 chunk 68 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 204 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 90 GLN B 185 GLN C 243 ASN D 185 GLN E 185 GLN A 41 ASN A 243 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 19240 Z= 0.160 Angle : 0.531 4.985 26155 Z= 0.288 Chirality : 0.043 0.148 2965 Planarity : 0.004 0.036 3235 Dihedral : 4.920 29.264 2565 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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 (0.16), residues: 2240 helix: -0.49 (0.18), residues: 610 sheet: 0.70 (0.20), residues: 645 loop : -0.56 (0.18), residues: 985 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 359 time to evaluate : 2.182 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 364 average time/residue: 1.3646 time to fit residues: 556.2665 Evaluate side-chains 343 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 330 time to evaluate : 2.165 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 6 residues processed: 8 average time/residue: 0.5456 time to fit residues: 8.7414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN C 243 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 19240 Z= 0.485 Angle : 0.726 6.495 26155 Z= 0.385 Chirality : 0.052 0.162 2965 Planarity : 0.006 0.066 3235 Dihedral : 5.796 35.690 2565 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2240 helix: 0.51 (0.20), residues: 615 sheet: 0.74 (0.20), residues: 650 loop : -0.07 (0.19), residues: 975 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 341 time to evaluate : 2.290 Fit side-chains outliers start: 44 outliers final: 27 residues processed: 352 average time/residue: 1.3961 time to fit residues: 550.7348 Evaluate side-chains 357 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 330 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 8 residues processed: 21 average time/residue: 0.6159 time to fit residues: 19.3248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 58 optimal weight: 0.0270 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 185 GLN B 243 ASN C 113 ASN C 243 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 19240 Z= 0.175 Angle : 0.534 5.903 26155 Z= 0.287 Chirality : 0.043 0.151 2965 Planarity : 0.003 0.035 3235 Dihedral : 5.261 31.221 2565 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 0.76 (0.17), residues: 2240 helix: 1.19 (0.21), residues: 615 sheet: 0.62 (0.19), residues: 665 loop : 0.09 (0.20), residues: 960 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 348 time to evaluate : 2.418 Fit side-chains outliers start: 31 outliers final: 21 residues processed: 362 average time/residue: 1.3587 time to fit residues: 552.0850 Evaluate side-chains 355 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 334 time to evaluate : 2.232 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 11 residues processed: 10 average time/residue: 0.5777 time to fit residues: 10.3878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 161 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 185 optimal weight: 0.0020 chunk 150 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 185 GLN C 113 ASN C 243 ASN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 19240 Z= 0.213 Angle : 0.543 6.735 26155 Z= 0.290 Chirality : 0.044 0.154 2965 Planarity : 0.004 0.035 3235 Dihedral : 5.200 29.537 2565 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer Outliers : 2.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 1.02 (0.18), residues: 2240 helix: 1.50 (0.22), residues: 615 sheet: 0.73 (0.19), residues: 670 loop : 0.23 (0.20), residues: 955 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 339 time to evaluate : 2.267 Fit side-chains outliers start: 45 outliers final: 26 residues processed: 355 average time/residue: 1.3429 time to fit residues: 534.5359 Evaluate side-chains 361 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 335 time to evaluate : 2.189 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 11 residues processed: 15 average time/residue: 0.4734 time to fit residues: 12.2137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 217 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 18 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 185 GLN C 113 ASN C 243 ASN C 265 ASN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 19240 Z= 0.369 Angle : 0.640 7.565 26155 Z= 0.340 Chirality : 0.049 0.159 2965 Planarity : 0.005 0.051 3235 Dihedral : 5.584 32.009 2565 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 0.95 (0.18), residues: 2240 helix: 1.39 (0.21), residues: 615 sheet: 0.58 (0.19), residues: 685 loop : 0.30 (0.20), residues: 940 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 344 time to evaluate : 2.292 Fit side-chains outliers start: 47 outliers final: 29 residues processed: 361 average time/residue: 1.3494 time to fit residues: 545.2080 Evaluate side-chains 367 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 338 time to evaluate : 2.053 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 15 residues processed: 16 average time/residue: 0.4069 time to fit residues: 11.7275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN C 113 ASN C 243 ASN C 265 ASN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 19240 Z= 0.175 Angle : 0.523 7.636 26155 Z= 0.280 Chirality : 0.043 0.148 2965 Planarity : 0.003 0.035 3235 Dihedral : 5.160 28.068 2565 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 1.12 (0.18), residues: 2240 helix: 1.66 (0.22), residues: 615 sheet: 0.64 (0.19), residues: 665 loop : 0.35 (0.20), residues: 960 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 343 time to evaluate : 2.283 Fit side-chains outliers start: 33 outliers final: 21 residues processed: 360 average time/residue: 1.3841 time to fit residues: 559.0343 Evaluate side-chains 351 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 330 time to evaluate : 2.092 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 7 average time/residue: 0.3281 time to fit residues: 6.5960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 0.0870 chunk 86 optimal weight: 0.0980 chunk 129 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN C 113 ASN C 243 ASN C 265 ASN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 19240 Z= 0.132 Angle : 0.486 7.659 26155 Z= 0.259 Chirality : 0.042 0.147 2965 Planarity : 0.003 0.052 3235 Dihedral : 4.804 22.862 2565 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 1.21 (0.18), residues: 2240 helix: 1.71 (0.22), residues: 620 sheet: 0.76 (0.19), residues: 670 loop : 0.37 (0.20), residues: 950 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 350 time to evaluate : 2.083 Fit side-chains outliers start: 34 outliers final: 20 residues processed: 367 average time/residue: 1.3411 time to fit residues: 551.9352 Evaluate side-chains 358 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 338 time to evaluate : 2.170 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 8 average time/residue: 0.3613 time to fit residues: 6.9439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 185 GLN C 41 ASN C 113 ASN C 243 ASN C 265 ASN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 19240 Z= 0.298 Angle : 0.595 8.002 26155 Z= 0.315 Chirality : 0.047 0.155 2965 Planarity : 0.004 0.041 3235 Dihedral : 5.244 27.196 2565 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 2240 helix: 1.58 (0.22), residues: 615 sheet: 0.67 (0.19), residues: 685 loop : 0.42 (0.20), residues: 940 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 334 time to evaluate : 2.279 Fit side-chains outliers start: 39 outliers final: 29 residues processed: 351 average time/residue: 1.3570 time to fit residues: 533.8988 Evaluate side-chains 362 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 333 time to evaluate : 2.455 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 13 residues processed: 18 average time/residue: 0.4949 time to fit residues: 14.7950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 224 optimal weight: 0.6980 chunk 206 optimal weight: 0.7980 chunk 178 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 109 optimal weight: 0.0470 chunk 141 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN C 265 ASN D 265 ASN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 19240 Z= 0.136 Angle : 0.501 7.980 26155 Z= 0.265 Chirality : 0.043 0.148 2965 Planarity : 0.003 0.054 3235 Dihedral : 4.851 23.255 2565 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 1.22 (0.18), residues: 2240 helix: 1.74 (0.22), residues: 615 sheet: 0.87 (0.20), residues: 640 loop : 0.28 (0.20), residues: 985 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 339 time to evaluate : 2.222 Fit side-chains outliers start: 20 outliers final: 15 residues processed: 351 average time/residue: 1.4081 time to fit residues: 552.9755 Evaluate side-chains 349 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 334 time to evaluate : 2.076 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 4 average time/residue: 0.2632 time to fit residues: 4.4804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 164 optimal weight: 0.9980 chunk 26 optimal weight: 0.0050 chunk 49 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN C 113 ASN C 243 ASN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.146988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.109716 restraints weight = 17535.267| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.99 r_work: 0.2805 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 19240 Z= 0.169 Angle : 0.520 8.042 26155 Z= 0.274 Chirality : 0.043 0.151 2965 Planarity : 0.004 0.058 3235 Dihedral : 4.896 24.073 2565 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 1.27 (0.18), residues: 2240 helix: 1.72 (0.22), residues: 615 sheet: 0.80 (0.19), residues: 670 loop : 0.43 (0.20), residues: 955 =============================================================================== Job complete usr+sys time: 8113.72 seconds wall clock time: 144 minutes 16.66 seconds (8656.66 seconds total)