Starting phenix.real_space_refine on Tue Feb 20 06:09:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mat_9063/02_2024/6mat_9063_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mat_9063/02_2024/6mat_9063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mat_9063/02_2024/6mat_9063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mat_9063/02_2024/6mat_9063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mat_9063/02_2024/6mat_9063_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mat_9063/02_2024/6mat_9063_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 P 33 5.49 5 S 124 5.16 5 C 16811 2.51 5 N 4824 2.21 5 O 5238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 474": "OE1" <-> "OE2" Residue "B PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 672": "OE1" <-> "OE2" Residue "E TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27030 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4454 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 4454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4454 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4454 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 4454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4454 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 4369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4369 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 537} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 4369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4369 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 537} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 135 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.85, per 1000 atoms: 0.59 Number of scatterers: 27030 At special positions: 0 Unit cell: (154.29, 154.29, 113.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 P 33 15.00 O 5238 8.00 N 4824 7.00 C 16811 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=0, symmetry=0 Time building additional restraints: 10.11 Conformation dependent library (CDL) restraints added in 5.4 seconds 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6446 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 12 sheets defined 49.3% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.12 Creating SS restraints... Processing helix chain 'A' and resid 208 through 223 removed outlier: 4.166A pdb=" N PHE A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 319 through 336 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 374 through 387 removed outlier: 5.267A pdb=" N ASP A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 408 through 437 removed outlier: 3.958A pdb=" N GLN A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASN A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 507 through 522 Proline residue: A 520 - end of helix Processing helix chain 'A' and resid 524 through 530 Processing helix chain 'A' and resid 548 through 558 Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 617 through 630 Processing helix chain 'A' and resid 652 through 655 No H-bonds generated for 'chain 'A' and resid 652 through 655' Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 716 through 724 Processing helix chain 'A' and resid 726 through 729 No H-bonds generated for 'chain 'A' and resid 726 through 729' Processing helix chain 'A' and resid 733 through 761 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 208 through 223 removed outlier: 4.179A pdb=" N PHE B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 319 through 336 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 374 through 387 removed outlier: 5.261A pdb=" N ASP B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 408 through 437 removed outlier: 3.964A pdb=" N GLN B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ASN B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 473 through 481 Processing helix chain 'B' and resid 500 through 502 No H-bonds generated for 'chain 'B' and resid 500 through 502' Processing helix chain 'B' and resid 507 through 522 Proline residue: B 520 - end of helix Processing helix chain 'B' and resid 524 through 530 Processing helix chain 'B' and resid 548 through 558 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 617 through 630 Processing helix chain 'B' and resid 652 through 655 No H-bonds generated for 'chain 'B' and resid 652 through 655' Processing helix chain 'B' and resid 671 through 681 Processing helix chain 'B' and resid 716 through 724 Processing helix chain 'B' and resid 726 through 729 No H-bonds generated for 'chain 'B' and resid 726 through 729' Processing helix chain 'B' and resid 733 through 761 Processing helix chain 'B' and resid 777 through 786 Processing helix chain 'B' and resid 795 through 799 Processing helix chain 'C' and resid 208 through 223 removed outlier: 4.156A pdb=" N PHE C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Proline residue: C 221 - end of helix Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'C' and resid 279 through 293 Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.788A pdb=" N ARG C 321 " --> pdb=" O GLY C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 374 through 387 removed outlier: 5.270A pdb=" N ASP C 387 " --> pdb=" O SER C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 408 through 437 removed outlier: 3.956A pdb=" N GLN C 424 " --> pdb=" O SER C 420 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ALA C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASN C 426 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 427 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 473 through 481 Processing helix chain 'C' and resid 500 through 502 No H-bonds generated for 'chain 'C' and resid 500 through 502' Processing helix chain 'C' and resid 507 through 522 Proline residue: C 520 - end of helix Processing helix chain 'C' and resid 524 through 530 Processing helix chain 'C' and resid 548 through 558 Processing helix chain 'C' and resid 579 through 592 Processing helix chain 'C' and resid 617 through 630 Processing helix chain 'C' and resid 652 through 655 No H-bonds generated for 'chain 'C' and resid 652 through 655' Processing helix chain 'C' and resid 671 through 681 Processing helix chain 'C' and resid 716 through 724 Processing helix chain 'C' and resid 726 through 729 No H-bonds generated for 'chain 'C' and resid 726 through 729' Processing helix chain 'C' and resid 733 through 761 Processing helix chain 'C' and resid 777 through 786 Processing helix chain 'C' and resid 795 through 799 Processing helix chain 'D' and resid 208 through 223 removed outlier: 4.162A pdb=" N PHE D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 225 through 231 Processing helix chain 'D' and resid 249 through 260 Processing helix chain 'D' and resid 279 through 293 Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.784A pdb=" N ARG D 321 " --> pdb=" O GLY D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 374 through 387 removed outlier: 5.260A pdb=" N ASP D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 408 through 437 removed outlier: 3.960A pdb=" N GLN D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ALA D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASN D 426 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE D 427 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 473 through 481 Processing helix chain 'D' and resid 500 through 502 No H-bonds generated for 'chain 'D' and resid 500 through 502' Processing helix chain 'D' and resid 507 through 522 Proline residue: D 520 - end of helix Processing helix chain 'D' and resid 524 through 530 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 579 through 592 Processing helix chain 'D' and resid 617 through 630 Processing helix chain 'D' and resid 652 through 655 No H-bonds generated for 'chain 'D' and resid 652 through 655' Processing helix chain 'D' and resid 671 through 681 Processing helix chain 'D' and resid 716 through 724 Processing helix chain 'D' and resid 726 through 729 No H-bonds generated for 'chain 'D' and resid 726 through 729' Processing helix chain 'D' and resid 733 through 761 Processing helix chain 'D' and resid 777 through 786 Processing helix chain 'D' and resid 795 through 799 Processing helix chain 'E' and resid 201 through 203 No H-bonds generated for 'chain 'E' and resid 201 through 203' Processing helix chain 'E' and resid 208 through 223 removed outlier: 4.176A pdb=" N PHE E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Proline residue: E 221 - end of helix Processing helix chain 'E' and resid 225 through 231 Processing helix chain 'E' and resid 249 through 260 Processing helix chain 'E' and resid 279 through 293 Processing helix chain 'E' and resid 319 through 336 Processing helix chain 'E' and resid 357 through 362 Processing helix chain 'E' and resid 374 through 387 removed outlier: 5.246A pdb=" N ASP E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 408 through 437 removed outlier: 3.967A pdb=" N GLN E 424 " --> pdb=" O SER E 420 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ALA E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASN E 426 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE E 427 " --> pdb=" O PHE E 423 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA E 436 " --> pdb=" O ALA E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 473 through 481 Processing helix chain 'E' and resid 500 through 502 No H-bonds generated for 'chain 'E' and resid 500 through 502' Processing helix chain 'E' and resid 507 through 522 Proline residue: E 520 - end of helix Processing helix chain 'E' and resid 524 through 530 Processing helix chain 'E' and resid 545 through 559 Processing helix chain 'E' and resid 578 through 592 Processing helix chain 'E' and resid 617 through 631 Processing helix chain 'E' and resid 652 through 655 No H-bonds generated for 'chain 'E' and resid 652 through 655' Processing helix chain 'E' and resid 671 through 681 Processing helix chain 'E' and resid 716 through 724 Processing helix chain 'E' and resid 726 through 729 No H-bonds generated for 'chain 'E' and resid 726 through 729' Processing helix chain 'E' and resid 733 through 761 Processing helix chain 'E' and resid 777 through 786 Processing helix chain 'F' and resid 208 through 223 removed outlier: 4.184A pdb=" N PHE F 220 " --> pdb=" O LYS F 216 " (cutoff:3.500A) Proline residue: F 221 - end of helix Processing helix chain 'F' and resid 225 through 231 Processing helix chain 'F' and resid 249 through 260 Processing helix chain 'F' and resid 279 through 293 Processing helix chain 'F' and resid 319 through 336 Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 374 through 387 removed outlier: 5.267A pdb=" N ASP F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 401 Processing helix chain 'F' and resid 408 through 437 removed outlier: 3.945A pdb=" N GLN F 424 " --> pdb=" O SER F 420 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASN F 426 " --> pdb=" O SER F 422 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE F 427 " --> pdb=" O PHE F 423 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA F 436 " --> pdb=" O ALA F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 473 through 481 Processing helix chain 'F' and resid 500 through 502 No H-bonds generated for 'chain 'F' and resid 500 through 502' Processing helix chain 'F' and resid 507 through 522 Proline residue: F 520 - end of helix Processing helix chain 'F' and resid 524 through 530 Processing helix chain 'F' and resid 548 through 558 Processing helix chain 'F' and resid 578 through 592 Processing helix chain 'F' and resid 617 through 631 Processing helix chain 'F' and resid 652 through 655 No H-bonds generated for 'chain 'F' and resid 652 through 655' Processing helix chain 'F' and resid 671 through 681 Processing helix chain 'F' and resid 716 through 724 Processing helix chain 'F' and resid 726 through 729 No H-bonds generated for 'chain 'F' and resid 726 through 729' Processing helix chain 'F' and resid 733 through 761 Processing helix chain 'F' and resid 777 through 786 Processing sheet with id= A, first strand: chain 'A' and resid 365 through 368 removed outlier: 8.514A pdb=" N VAL A 239 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 345 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU A 241 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA A 347 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS A 297 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU A 346 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE A 299 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ALA A 348 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 301 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA A 263 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE A 300 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 265 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ASP A 302 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 267 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 662 through 665 removed outlier: 3.650A pdb=" N THR A 662 " --> pdb=" O GLY A 537 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE A 538 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 640 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU A 540 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY A 642 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS A 596 " --> pdb=" O TYR A 639 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE A 641 " --> pdb=" O CYS A 596 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU A 598 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ALA A 643 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE A 600 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 562 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE A 599 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE A 564 " --> pdb=" O PHE A 599 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP A 601 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 566 " --> pdb=" O ASP A 601 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 365 through 368 removed outlier: 8.517A pdb=" N VAL B 239 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 345 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU B 241 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA B 347 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N CYS B 297 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU B 346 " --> pdb=" O CYS B 297 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE B 299 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA B 348 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU B 301 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA B 263 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE B 300 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE B 265 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASP B 302 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 267 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 662 through 665 removed outlier: 3.627A pdb=" N THR B 662 " --> pdb=" O GLY B 537 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N ILE B 538 " --> pdb=" O ILE B 638 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B 640 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU B 540 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY B 642 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N CYS B 596 " --> pdb=" O TYR B 639 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE B 641 " --> pdb=" O CYS B 596 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU B 598 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALA B 643 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE B 600 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN B 562 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE B 599 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE B 564 " --> pdb=" O PHE B 599 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP B 601 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 566 " --> pdb=" O ASP B 601 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.529A pdb=" N VAL C 239 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 345 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU C 241 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA C 347 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N CYS C 297 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU C 346 " --> pdb=" O CYS C 297 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE C 299 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA C 348 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU C 301 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA C 263 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE C 300 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 265 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASP C 302 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 267 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 662 through 665 removed outlier: 3.646A pdb=" N THR C 662 " --> pdb=" O GLY C 537 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ILE C 538 " --> pdb=" O ILE C 638 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C 640 " --> pdb=" O ILE C 538 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LEU C 540 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY C 642 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS C 596 " --> pdb=" O TYR C 639 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE C 641 " --> pdb=" O CYS C 596 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU C 598 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ALA C 643 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE C 600 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN C 562 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N PHE C 599 " --> pdb=" O ASN C 562 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE C 564 " --> pdb=" O PHE C 599 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASP C 601 " --> pdb=" O ILE C 564 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE C 566 " --> pdb=" O ASP C 601 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.527A pdb=" N VAL D 239 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL D 345 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU D 241 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA D 347 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS D 297 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU D 346 " --> pdb=" O CYS D 297 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE D 299 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA D 348 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU D 301 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA D 263 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE D 300 " --> pdb=" O ALA D 263 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE D 265 " --> pdb=" O PHE D 300 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP D 302 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL D 267 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 662 through 665 removed outlier: 3.648A pdb=" N THR D 662 " --> pdb=" O GLY D 537 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ILE D 538 " --> pdb=" O ILE D 638 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL D 640 " --> pdb=" O ILE D 538 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU D 540 " --> pdb=" O VAL D 640 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY D 642 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N CYS D 596 " --> pdb=" O TYR D 639 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE D 641 " --> pdb=" O CYS D 596 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU D 598 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA D 643 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE D 600 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN D 562 " --> pdb=" O ILE D 597 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE D 599 " --> pdb=" O ASN D 562 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE D 564 " --> pdb=" O PHE D 599 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP D 601 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE D 566 " --> pdb=" O ASP D 601 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.517A pdb=" N VAL E 239 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL E 345 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU E 241 " --> pdb=" O VAL E 345 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA E 347 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS E 297 " --> pdb=" O VAL E 344 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU E 346 " --> pdb=" O CYS E 297 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE E 299 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ALA E 348 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU E 301 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA E 263 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE E 300 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE E 265 " --> pdb=" O PHE E 300 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASP E 302 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL E 267 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 662 through 665 removed outlier: 3.671A pdb=" N THR E 662 " --> pdb=" O GLY E 537 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N ILE E 538 " --> pdb=" O ILE E 638 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL E 640 " --> pdb=" O ILE E 538 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LEU E 540 " --> pdb=" O VAL E 640 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY E 642 " --> pdb=" O LEU E 540 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N CYS E 596 " --> pdb=" O TYR E 639 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE E 641 " --> pdb=" O CYS E 596 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU E 598 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ALA E 643 " --> pdb=" O LEU E 598 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE E 600 " --> pdb=" O ALA E 643 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN E 562 " --> pdb=" O ILE E 597 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE E 599 " --> pdb=" O ASN E 562 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE E 564 " --> pdb=" O PHE E 599 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP E 601 " --> pdb=" O ILE E 564 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE E 566 " --> pdb=" O ASP E 601 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 365 through 368 removed outlier: 8.511A pdb=" N VAL F 239 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL F 345 " --> pdb=" O VAL F 239 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU F 241 " --> pdb=" O VAL F 345 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA F 347 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N CYS F 297 " --> pdb=" O VAL F 344 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU F 346 " --> pdb=" O CYS F 297 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE F 299 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA F 348 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU F 301 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA F 263 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N PHE F 300 " --> pdb=" O ALA F 263 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE F 265 " --> pdb=" O PHE F 300 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP F 302 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL F 267 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 662 through 666 removed outlier: 3.716A pdb=" N THR F 662 " --> pdb=" O GLY F 537 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ILE F 538 " --> pdb=" O ILE F 638 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL F 640 " --> pdb=" O ILE F 538 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU F 540 " --> pdb=" O VAL F 640 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY F 642 " --> pdb=" O LEU F 540 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N GLY F 542 " --> pdb=" O GLY F 642 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR F 644 " --> pdb=" O GLY F 542 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N CYS F 596 " --> pdb=" O TYR F 639 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE F 641 " --> pdb=" O CYS F 596 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU F 598 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA F 643 " --> pdb=" O LEU F 598 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE F 600 " --> pdb=" O ALA F 643 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN F 562 " --> pdb=" O ILE F 597 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE F 599 " --> pdb=" O ASN F 562 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE F 564 " --> pdb=" O PHE F 599 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP F 601 " --> pdb=" O ILE F 564 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE F 566 " --> pdb=" O ASP F 601 " (cutoff:3.500A) 1095 hydrogen bonds defined for protein. 3267 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: 9.43 Time building geometry restraints manager: 10.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8907 1.34 - 1.47: 4117 1.47 - 1.59: 14194 1.59 - 1.72: 59 1.72 - 1.85: 206 Bond restraints: 27483 Sorted by residual: bond pdb=" C4 ATP B 902 " pdb=" C5 ATP B 902 " ideal model delta sigma weight residual 1.388 1.478 -0.090 1.00e-02 1.00e+04 8.06e+01 bond pdb=" C5 ATP B 902 " pdb=" C6 ATP B 902 " ideal model delta sigma weight residual 1.409 1.498 -0.089 1.00e-02 1.00e+04 7.98e+01 bond pdb=" C4 ATP C 901 " pdb=" C5 ATP C 901 " ideal model delta sigma weight residual 1.388 1.474 -0.086 1.00e-02 1.00e+04 7.43e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.474 -0.086 1.00e-02 1.00e+04 7.39e+01 bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.27e+01 ... (remaining 27478 not shown) Histogram of bond angle deviations from ideal: 96.02 - 104.16: 822 104.16 - 112.29: 12207 112.29 - 120.43: 13040 120.43 - 128.57: 10974 128.57 - 136.70: 199 Bond angle restraints: 37242 Sorted by residual: angle pdb=" PB ATP C 902 " pdb=" O3B ATP C 902 " pdb=" PG ATP C 902 " ideal model delta sigma weight residual 139.87 118.42 21.45 1.00e+00 1.00e+00 4.60e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 118.91 20.96 1.00e+00 1.00e+00 4.39e+02 angle pdb=" PB ATP A 902 " pdb=" O3B ATP A 902 " pdb=" PG ATP A 902 " ideal model delta sigma weight residual 139.87 118.92 20.95 1.00e+00 1.00e+00 4.39e+02 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 119.45 20.42 1.00e+00 1.00e+00 4.17e+02 angle pdb=" PB ATP D 902 " pdb=" O3B ATP D 902 " pdb=" PG ATP D 902 " ideal model delta sigma weight residual 139.87 119.47 20.40 1.00e+00 1.00e+00 4.16e+02 ... (remaining 37237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 15321 18.02 - 36.04: 1082 36.04 - 54.06: 374 54.06 - 72.08: 146 72.08 - 90.09: 219 Dihedral angle restraints: 17142 sinusoidal: 7182 harmonic: 9960 Sorted by residual: dihedral pdb=" C THR F 337 " pdb=" N THR F 337 " pdb=" CA THR F 337 " pdb=" CB THR F 337 " ideal model delta harmonic sigma weight residual -122.00 -134.43 12.43 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" C THR A 337 " pdb=" N THR A 337 " pdb=" CA THR A 337 " pdb=" CB THR A 337 " ideal model delta harmonic sigma weight residual -122.00 -134.24 12.24 0 2.50e+00 1.60e-01 2.40e+01 dihedral pdb=" C THR B 337 " pdb=" N THR B 337 " pdb=" CA THR B 337 " pdb=" CB THR B 337 " ideal model delta harmonic sigma weight residual -122.00 -134.23 12.23 0 2.50e+00 1.60e-01 2.39e+01 ... (remaining 17139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 3414 0.143 - 0.286: 710 0.286 - 0.428: 84 0.428 - 0.571: 10 0.571 - 0.714: 1 Chirality restraints: 4219 Sorted by residual: chirality pdb=" CA PRO E 544 " pdb=" N PRO E 544 " pdb=" C PRO E 544 " pdb=" CB PRO E 544 " both_signs ideal model delta sigma weight residual False 2.72 2.00 0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CA SER C 636 " pdb=" N SER C 636 " pdb=" C SER C 636 " pdb=" CB SER C 636 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CA THR B 337 " pdb=" N THR B 337 " pdb=" C THR B 337 " pdb=" CB THR B 337 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.45 2.00e-01 2.50e+01 4.98e+00 ... (remaining 4216 not shown) Planarity restraints: 4825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 639 " -0.101 2.00e-02 2.50e+03 5.25e-02 5.51e+01 pdb=" CG TYR D 639 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR D 639 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR D 639 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR D 639 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR D 639 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR D 639 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 639 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 639 " 0.100 2.00e-02 2.50e+03 5.20e-02 5.41e+01 pdb=" CG TYR B 639 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 639 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR B 639 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR B 639 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR B 639 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR B 639 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 639 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 639 " -0.093 2.00e-02 2.50e+03 4.83e-02 4.67e+01 pdb=" CG TYR C 639 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR C 639 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR C 639 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR C 639 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR C 639 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR C 639 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 639 " -0.067 2.00e-02 2.50e+03 ... (remaining 4822 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 8059 2.90 - 3.40: 24983 3.40 - 3.90: 41183 3.90 - 4.40: 45765 4.40 - 4.90: 78474 Nonbonded interactions: 198464 Sorted by model distance: nonbonded pdb=" O PRO E 543 " pdb=" CA PRO E 544 " model vdw 2.397 2.776 nonbonded pdb=" O GLY A 258 " pdb=" NH2 ARG F 460 " model vdw 2.413 2.520 nonbonded pdb=" O ASN E 557 " pdb=" N LYS E 560 " model vdw 2.480 2.520 nonbonded pdb=" O ARG E 460 " pdb=" NH2 ARG F 223 " model vdw 2.482 2.520 nonbonded pdb=" NH2 ARG C 659 " pdb=" O1G ATP B 901 " model vdw 2.486 2.520 ... (remaining 198459 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 193 through 790 or resid 902)) selection = (chain 'B' and (resid 193 through 790 or resid 902)) selection = (chain 'C' and (resid 193 through 790 or resid 902)) selection = (chain 'D' and (resid 193 through 790 or resid 902)) selection = chain 'E' selection = (chain 'F' and (resid 193 through 790 or resid 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 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: 3.380 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 74.400 Find NCS groups from input model: 2.290 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 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 : 0.012 0.090 27483 Z= 0.821 Angle : 1.798 21.450 37242 Z= 1.254 Chirality : 0.114 0.714 4219 Planarity : 0.010 0.111 4825 Dihedral : 19.221 90.095 10696 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 2.02 % Allowed : 6.36 % Favored : 91.62 % Rotamer: Outliers : 2.79 % Allowed : 8.90 % Favored : 88.31 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 6.52 % 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: -1.24 (0.13), residues: 3412 helix: 0.24 (0.10), residues: 1876 sheet: -0.37 (0.25), residues: 407 loop : -2.82 (0.16), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.009 TRP E 453 HIS 0.001 0.000 HIS F 254 PHE 0.041 0.007 PHE D 527 TYR 0.101 0.009 TYR D 639 ARG 0.021 0.002 ARG F 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 913 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ILE cc_start: 0.9106 (mp) cc_final: 0.8410 (tp) REVERT: A 350 ASN cc_start: 0.7720 (m-40) cc_final: 0.7367 (t0) REVERT: A 485 PRO cc_start: 0.5604 (Cg_endo) cc_final: 0.4732 (Cg_exo) REVERT: A 495 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8338 (tp) REVERT: A 599 PHE cc_start: 0.8921 (t80) cc_final: 0.8021 (t80) REVERT: A 738 ASN cc_start: 0.9166 (t0) cc_final: 0.8947 (t0) REVERT: B 231 MET cc_start: 0.8937 (mtt) cc_final: 0.8513 (mtm) REVERT: B 240 LEU cc_start: 0.8904 (tp) cc_final: 0.8329 (mt) REVERT: B 292 ILE cc_start: 0.9186 (pt) cc_final: 0.8499 (mt) REVERT: B 325 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7407 (tp30) REVERT: B 380 ILE cc_start: 0.8954 (mt) cc_final: 0.8685 (mm) REVERT: B 500 TRP cc_start: 0.8230 (m100) cc_final: 0.7081 (m100) REVERT: B 627 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8339 (m) REVERT: B 639 TYR cc_start: 0.8178 (m-80) cc_final: 0.7821 (m-10) REVERT: B 656 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.6720 (tmm160) REVERT: B 664 ILE cc_start: 0.9098 (mt) cc_final: 0.8852 (mm) REVERT: B 731 PHE cc_start: 0.8331 (m-10) cc_final: 0.7757 (m-80) REVERT: B 780 TRP cc_start: 0.8244 (OUTLIER) cc_final: 0.7904 (m100) REVERT: B 798 MET cc_start: 0.8282 (mmm) cc_final: 0.8002 (mmt) REVERT: C 284 ILE cc_start: 0.8534 (mt) cc_final: 0.7988 (mt) REVERT: C 345 VAL cc_start: 0.9077 (t) cc_final: 0.8394 (t) REVERT: C 388 LEU cc_start: 0.8859 (mp) cc_final: 0.8470 (mp) REVERT: C 407 VAL cc_start: 0.6334 (OUTLIER) cc_final: 0.5920 (m) REVERT: C 656 ARG cc_start: 0.6515 (OUTLIER) cc_final: 0.6118 (tmm-80) REVERT: C 740 MET cc_start: 0.8987 (tmm) cc_final: 0.8756 (tmm) REVERT: D 264 PHE cc_start: 0.7852 (t80) cc_final: 0.7008 (t80) REVERT: D 292 ILE cc_start: 0.8833 (pt) cc_final: 0.8347 (mt) REVERT: D 354 PHE cc_start: 0.7851 (t80) cc_final: 0.7600 (t80) REVERT: D 355 LEU cc_start: 0.9181 (mt) cc_final: 0.8930 (mt) REVERT: D 495 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8796 (tp) REVERT: D 627 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8645 (m) REVERT: D 682 TYR cc_start: 0.8148 (t80) cc_final: 0.7778 (t80) REVERT: D 727 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6092 (mtm-85) REVERT: E 325 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7204 (tp30) REVERT: E 350 ASN cc_start: 0.8347 (m-40) cc_final: 0.7857 (p0) REVERT: E 402 MET cc_start: 0.7532 (mmm) cc_final: 0.6910 (ptm) REVERT: E 473 MET cc_start: 0.8530 (tpt) cc_final: 0.8275 (tpt) REVERT: E 488 LYS cc_start: 0.7928 (pttm) cc_final: 0.7221 (tppt) REVERT: E 495 ILE cc_start: -0.0492 (OUTLIER) cc_final: -0.1130 (tp) REVERT: E 597 ILE cc_start: 0.9288 (mp) cc_final: 0.9022 (mp) REVERT: E 599 PHE cc_start: 0.7901 (t80) cc_final: 0.7655 (t80) REVERT: F 369 MET cc_start: 0.5268 (mtp) cc_final: 0.4837 (mpp) REVERT: F 623 ASN cc_start: 0.7815 (m-40) cc_final: 0.7521 (m-40) REVERT: F 639 TYR cc_start: 0.7298 (m-80) cc_final: 0.6972 (m-10) REVERT: F 760 LYS cc_start: 0.7660 (mttt) cc_final: 0.7124 (pptt) outliers start: 80 outliers final: 15 residues processed: 970 average time/residue: 0.4564 time to fit residues: 655.1883 Evaluate side-chains 444 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 417 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 8.9990 chunk 259 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 268 optimal weight: 6.9990 chunk 103 optimal weight: 0.0000 chunk 162 optimal weight: 20.0000 chunk 199 optimal weight: 0.9980 chunk 310 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN A 438 HIS A 445 ASN A 502 HIS A 573 ASN A 585 GLN B 254 HIS B 445 ASN B 484 GLN B 502 HIS ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 HIS C 342 ASN C 445 ASN C 502 HIS C 557 ASN C 573 ASN C 623 ASN C 745 GLN D 254 HIS D 328 ASN D 335 GLN D 342 ASN D 395 ASN D 424 GLN D 445 ASN D 502 HIS ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 ASN E 502 HIS ** E 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 785 ASN F 395 ASN ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 ASN F 502 HIS ** F 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 27483 Z= 0.265 Angle : 0.766 8.770 37242 Z= 0.398 Chirality : 0.045 0.272 4219 Planarity : 0.007 0.088 4825 Dihedral : 12.035 88.872 4140 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.25 % Favored : 94.43 % Rotamer: Outliers : 0.35 % Allowed : 4.43 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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 (0.14), residues: 3412 helix: 1.56 (0.12), residues: 1819 sheet: 0.15 (0.24), residues: 423 loop : -2.40 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 780 HIS 0.011 0.001 HIS E 254 PHE 0.025 0.002 PHE E 600 TYR 0.017 0.002 TYR F 639 ARG 0.006 0.001 ARG F 581 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 510 time to evaluate : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.8409 (tmm) cc_final: 0.8095 (tmm) REVERT: A 388 LEU cc_start: 0.8520 (tp) cc_final: 0.8229 (tt) REVERT: A 738 ASN cc_start: 0.9169 (t0) cc_final: 0.8964 (t0) REVERT: A 740 MET cc_start: 0.8646 (tmm) cc_final: 0.8318 (tmm) REVERT: B 231 MET cc_start: 0.9138 (mtt) cc_final: 0.8677 (mtt) REVERT: B 240 LEU cc_start: 0.8989 (tp) cc_final: 0.8407 (mt) REVERT: B 616 ASP cc_start: 0.8100 (p0) cc_final: 0.7629 (p0) REVERT: B 798 MET cc_start: 0.8344 (mmm) cc_final: 0.8083 (mmm) REVERT: C 662 THR cc_start: 0.7790 (m) cc_final: 0.7394 (m) REVERT: C 740 MET cc_start: 0.9079 (tmm) cc_final: 0.8682 (tmm) REVERT: D 677 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8613 (tt) REVERT: D 682 TYR cc_start: 0.8350 (t80) cc_final: 0.7713 (t80) REVERT: E 318 MET cc_start: 0.8261 (ppp) cc_final: 0.7725 (ppp) REVERT: E 369 MET cc_start: 0.7906 (ttm) cc_final: 0.7633 (ttm) REVERT: E 402 MET cc_start: 0.7822 (mmm) cc_final: 0.6890 (ptm) REVERT: E 427 ILE cc_start: 0.6217 (mp) cc_final: 0.5745 (mp) REVERT: E 488 LYS cc_start: 0.7734 (pttm) cc_final: 0.7252 (tppt) REVERT: E 599 PHE cc_start: 0.8198 (t80) cc_final: 0.7483 (t80) REVERT: F 235 TYR cc_start: 0.3628 (p90) cc_final: 0.3415 (p90) REVERT: F 369 MET cc_start: 0.5456 (mtp) cc_final: 0.4135 (tpp) REVERT: F 452 ASP cc_start: 0.8511 (m-30) cc_final: 0.8068 (m-30) REVERT: F 623 ASN cc_start: 0.8078 (m-40) cc_final: 0.7582 (m-40) REVERT: F 639 TYR cc_start: 0.7565 (m-80) cc_final: 0.7156 (m-10) REVERT: F 777 MET cc_start: 0.8903 (tpt) cc_final: 0.8549 (tpp) outliers start: 10 outliers final: 0 residues processed: 517 average time/residue: 0.4446 time to fit residues: 345.0404 Evaluate side-chains 299 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 298 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 258 optimal weight: 0.5980 chunk 211 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 311 optimal weight: 20.0000 chunk 336 optimal weight: 5.9990 chunk 277 optimal weight: 0.0370 chunk 308 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 overall best weight: 4.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN A 438 HIS A 573 ASN B 242 HIS B 602 GLN B 745 GLN C 303 GLN C 328 ASN C 450 GLN D 342 ASN D 395 ASN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 ASN E 303 GLN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 ASN F 557 ASN F 573 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27483 Z= 0.270 Angle : 0.687 14.314 37242 Z= 0.354 Chirality : 0.043 0.220 4219 Planarity : 0.007 0.113 4825 Dihedral : 11.917 89.445 4140 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.24 % Favored : 93.49 % Rotamer: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3412 helix: 1.58 (0.12), residues: 1859 sheet: 0.50 (0.25), residues: 422 loop : -1.95 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 541 HIS 0.011 0.001 HIS D 459 PHE 0.035 0.002 PHE A 731 TYR 0.023 0.002 TYR A 413 ARG 0.012 0.001 ARG F 759 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 381 time to evaluate : 3.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 TYR cc_start: 0.7631 (m-10) cc_final: 0.7254 (m-10) REVERT: A 740 MET cc_start: 0.8684 (tmm) cc_final: 0.8306 (tmm) REVERT: A 798 MET cc_start: 0.6773 (tmm) cc_final: 0.6511 (tmm) REVERT: B 231 MET cc_start: 0.9192 (mtt) cc_final: 0.8560 (mtt) REVERT: B 292 ILE cc_start: 0.9495 (pt) cc_final: 0.8985 (mt) REVERT: B 318 MET cc_start: 0.7054 (mmm) cc_final: 0.6826 (mmm) REVERT: B 361 ARG cc_start: 0.7621 (mmp-170) cc_final: 0.7393 (mmp80) REVERT: B 616 ASP cc_start: 0.8273 (p0) cc_final: 0.7566 (p0) REVERT: B 798 MET cc_start: 0.8345 (mmm) cc_final: 0.8114 (mmm) REVERT: C 740 MET cc_start: 0.9065 (tmm) cc_final: 0.8813 (tmm) REVERT: E 279 GLU cc_start: 0.8225 (tt0) cc_final: 0.7631 (tm-30) REVERT: E 318 MET cc_start: 0.8051 (ppp) cc_final: 0.7563 (ppp) REVERT: E 402 MET cc_start: 0.7867 (mmm) cc_final: 0.6768 (ptm) REVERT: E 427 ILE cc_start: 0.6236 (mp) cc_final: 0.5836 (mp) REVERT: E 452 ASP cc_start: 0.7488 (m-30) cc_final: 0.7081 (m-30) REVERT: E 473 MET cc_start: 0.7975 (tpt) cc_final: 0.7698 (tpp) REVERT: E 488 LYS cc_start: 0.7988 (pttm) cc_final: 0.7251 (tppt) REVERT: E 500 TRP cc_start: 0.7783 (m100) cc_final: 0.6728 (m100) REVERT: E 599 PHE cc_start: 0.7822 (t80) cc_final: 0.7058 (t80) REVERT: F 235 TYR cc_start: 0.3723 (p90) cc_final: 0.3431 (p90) REVERT: F 362 ARG cc_start: 0.7046 (mmp-170) cc_final: 0.6217 (mmt180) REVERT: F 369 MET cc_start: 0.5682 (mtp) cc_final: 0.4384 (tpp) REVERT: F 525 GLU cc_start: 0.8189 (pm20) cc_final: 0.7862 (pm20) REVERT: F 623 ASN cc_start: 0.8182 (m-40) cc_final: 0.7768 (m-40) REVERT: F 639 TYR cc_start: 0.7792 (m-80) cc_final: 0.7368 (m-10) REVERT: F 740 MET cc_start: 0.8343 (ppp) cc_final: 0.8045 (ppp) REVERT: F 777 MET cc_start: 0.8766 (tpt) cc_final: 0.8187 (tpp) outliers start: 3 outliers final: 0 residues processed: 382 average time/residue: 0.4612 time to fit residues: 272.1153 Evaluate side-chains 261 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 312 optimal weight: 1.9990 chunk 330 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 295 optimal weight: 0.0270 chunk 89 optimal weight: 0.5980 overall best weight: 2.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN B 602 GLN C 328 ASN ** C 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 785 ASN ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 HIS ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 GLN ** E 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 573 ASN F 745 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27483 Z= 0.209 Angle : 0.618 10.501 37242 Z= 0.314 Chirality : 0.041 0.206 4219 Planarity : 0.006 0.090 4825 Dihedral : 11.682 89.635 4140 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.57 % Favored : 94.17 % Rotamer: Outliers : 0.10 % Allowed : 3.77 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 3412 helix: 1.65 (0.12), residues: 1861 sheet: 0.62 (0.25), residues: 417 loop : -1.78 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 780 HIS 0.010 0.001 HIS E 254 PHE 0.015 0.002 PHE F 423 TYR 0.018 0.001 TYR F 413 ARG 0.013 0.001 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 371 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 TYR cc_start: 0.7570 (m-10) cc_final: 0.7362 (m-10) REVERT: A 576 VAL cc_start: 0.8474 (m) cc_final: 0.8259 (p) REVERT: A 677 ILE cc_start: 0.9495 (pt) cc_final: 0.9258 (tt) REVERT: A 740 MET cc_start: 0.8622 (tmm) cc_final: 0.8270 (tmm) REVERT: B 231 MET cc_start: 0.9054 (mtt) cc_final: 0.8607 (mtt) REVERT: B 292 ILE cc_start: 0.9411 (pt) cc_final: 0.8919 (mt) REVERT: B 361 ARG cc_start: 0.7759 (mmp-170) cc_final: 0.7286 (mmp80) REVERT: B 616 ASP cc_start: 0.8341 (p0) cc_final: 0.7492 (p0) REVERT: B 798 MET cc_start: 0.8324 (mmm) cc_final: 0.8093 (mmm) REVERT: C 264 PHE cc_start: 0.8526 (t80) cc_final: 0.8231 (t80) REVERT: C 740 MET cc_start: 0.9092 (tmm) cc_final: 0.8814 (tmm) REVERT: D 473 MET cc_start: 0.8413 (mmm) cc_final: 0.8185 (mmm) REVERT: D 677 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8732 (tt) REVERT: E 279 GLU cc_start: 0.8440 (tt0) cc_final: 0.7630 (tm-30) REVERT: E 318 MET cc_start: 0.8157 (ppp) cc_final: 0.7692 (ppp) REVERT: E 402 MET cc_start: 0.7847 (mmm) cc_final: 0.6899 (ptm) REVERT: E 427 ILE cc_start: 0.6472 (mp) cc_final: 0.6035 (mm) REVERT: E 452 ASP cc_start: 0.7664 (m-30) cc_final: 0.7297 (m-30) REVERT: E 473 MET cc_start: 0.7952 (tpt) cc_final: 0.7674 (tpp) REVERT: E 488 LYS cc_start: 0.7923 (pttm) cc_final: 0.7294 (tppt) REVERT: E 581 ARG cc_start: 0.7776 (ttt180) cc_final: 0.7553 (tpp-160) REVERT: E 599 PHE cc_start: 0.7922 (t80) cc_final: 0.6940 (t80) REVERT: E 604 ASP cc_start: 0.7653 (p0) cc_final: 0.7406 (p0) REVERT: F 235 TYR cc_start: 0.3905 (p90) cc_final: 0.3637 (p90) REVERT: F 362 ARG cc_start: 0.7175 (mmp-170) cc_final: 0.6455 (mmt90) REVERT: F 369 MET cc_start: 0.5636 (mtp) cc_final: 0.4080 (tpp) REVERT: F 623 ASN cc_start: 0.8140 (m-40) cc_final: 0.7755 (m-40) REVERT: F 639 TYR cc_start: 0.7769 (m-80) cc_final: 0.7436 (m-10) REVERT: F 740 MET cc_start: 0.8379 (ppp) cc_final: 0.8097 (ppp) REVERT: F 777 MET cc_start: 0.8799 (tpt) cc_final: 0.8551 (tpp) outliers start: 3 outliers final: 0 residues processed: 372 average time/residue: 0.4127 time to fit residues: 240.6556 Evaluate side-chains 262 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 5.9990 chunk 187 optimal weight: 0.0070 chunk 4 optimal weight: 10.0000 chunk 246 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 282 optimal weight: 7.9990 chunk 228 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 296 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 684 ASN ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 799 HIS E 254 HIS ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 684 ASN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.6593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27483 Z= 0.235 Angle : 0.632 13.969 37242 Z= 0.319 Chirality : 0.042 0.273 4219 Planarity : 0.006 0.096 4825 Dihedral : 11.400 89.828 4140 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.42 % Favored : 93.35 % Rotamer: Outliers : 0.07 % Allowed : 3.31 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.66 (0.15), residues: 3412 helix: 1.59 (0.12), residues: 1863 sheet: 0.65 (0.25), residues: 414 loop : -1.63 (0.20), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 219 HIS 0.009 0.001 HIS C 459 PHE 0.022 0.002 PHE C 423 TYR 0.025 0.002 TYR C 233 ARG 0.006 0.001 ARG D 510 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 348 time to evaluate : 3.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.8205 (tpt) cc_final: 0.7770 (tpp) REVERT: A 616 ASP cc_start: 0.7961 (p0) cc_final: 0.7758 (p0) REVERT: A 740 MET cc_start: 0.8580 (tmm) cc_final: 0.8288 (tmm) REVERT: B 231 MET cc_start: 0.9022 (mtt) cc_final: 0.8670 (mtt) REVERT: B 292 ILE cc_start: 0.9445 (pt) cc_final: 0.8978 (mt) REVERT: B 318 MET cc_start: 0.7192 (mmm) cc_final: 0.6823 (mmm) REVERT: B 616 ASP cc_start: 0.8271 (p0) cc_final: 0.7300 (p0) REVERT: B 798 MET cc_start: 0.8234 (mmm) cc_final: 0.8026 (mmm) REVERT: C 740 MET cc_start: 0.9150 (tmm) cc_final: 0.8854 (tmm) REVERT: D 473 MET cc_start: 0.8333 (mmm) cc_final: 0.8040 (mmm) REVERT: D 677 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8845 (tt) REVERT: E 318 MET cc_start: 0.8366 (ppp) cc_final: 0.7969 (ppp) REVERT: E 327 MET cc_start: 0.8187 (tpp) cc_final: 0.7905 (mmm) REVERT: E 361 ARG cc_start: 0.8661 (mmt180) cc_final: 0.8304 (mmm-85) REVERT: E 402 MET cc_start: 0.7902 (mmm) cc_final: 0.6819 (ptm) REVERT: E 452 ASP cc_start: 0.8006 (m-30) cc_final: 0.7650 (m-30) REVERT: E 473 MET cc_start: 0.7961 (tpt) cc_final: 0.7612 (tpp) REVERT: E 488 LYS cc_start: 0.7932 (pttm) cc_final: 0.7269 (tppt) REVERT: E 599 PHE cc_start: 0.7919 (t80) cc_final: 0.6903 (t80) REVERT: F 307 ILE cc_start: 0.4372 (mt) cc_final: 0.4114 (mp) REVERT: F 362 ARG cc_start: 0.7296 (mmp-170) cc_final: 0.6268 (mmt90) REVERT: F 369 MET cc_start: 0.5715 (mtp) cc_final: 0.4036 (tpp) REVERT: F 371 MET cc_start: 0.6052 (ppp) cc_final: 0.5809 (ppp) REVERT: F 525 GLU cc_start: 0.8373 (pm20) cc_final: 0.8031 (pm20) REVERT: F 623 ASN cc_start: 0.8160 (m-40) cc_final: 0.7878 (m-40) REVERT: F 639 TYR cc_start: 0.7979 (m-80) cc_final: 0.7713 (m-10) REVERT: F 740 MET cc_start: 0.8312 (ppp) cc_final: 0.8093 (ppp) REVERT: F 777 MET cc_start: 0.8595 (tpt) cc_final: 0.8272 (tpp) outliers start: 2 outliers final: 0 residues processed: 348 average time/residue: 0.4012 time to fit residues: 219.6973 Evaluate side-chains 249 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 6.9990 chunk 297 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 330 optimal weight: 0.0030 chunk 274 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 ASN D 342 ASN ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 ASN E 254 HIS ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 ASN ** F 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.6877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27483 Z= 0.201 Angle : 0.595 8.223 37242 Z= 0.302 Chirality : 0.041 0.204 4219 Planarity : 0.006 0.091 4825 Dihedral : 11.183 88.816 4140 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.69 % Favored : 94.11 % Rotamer: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.74 (0.15), residues: 3412 helix: 1.62 (0.12), residues: 1859 sheet: 0.69 (0.26), residues: 413 loop : -1.53 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 780 HIS 0.010 0.001 HIS B 799 PHE 0.016 0.002 PHE F 527 TYR 0.030 0.001 TYR D 752 ARG 0.011 0.001 ARG E 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 343 time to evaluate : 3.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 TYR cc_start: 0.7694 (m-10) cc_final: 0.7203 (m-10) REVERT: A 473 MET cc_start: 0.8174 (tpt) cc_final: 0.7747 (tpp) REVERT: A 485 PRO cc_start: 0.6590 (Cg_endo) cc_final: 0.6355 (Cg_exo) REVERT: A 616 ASP cc_start: 0.8057 (p0) cc_final: 0.7773 (p0) REVERT: A 740 MET cc_start: 0.8579 (tmm) cc_final: 0.8169 (tmm) REVERT: B 231 MET cc_start: 0.8974 (mtt) cc_final: 0.8672 (mtt) REVERT: B 292 ILE cc_start: 0.9433 (pt) cc_final: 0.8957 (mt) REVERT: B 318 MET cc_start: 0.7176 (mmm) cc_final: 0.6962 (mmm) REVERT: B 616 ASP cc_start: 0.8242 (p0) cc_final: 0.7217 (p0) REVERT: B 798 MET cc_start: 0.8290 (mmm) cc_final: 0.7991 (mmm) REVERT: C 233 TYR cc_start: 0.7136 (m-10) cc_final: 0.6765 (m-80) REVERT: C 740 MET cc_start: 0.9154 (tmm) cc_final: 0.8838 (tmm) REVERT: E 318 MET cc_start: 0.8359 (ppp) cc_final: 0.8005 (ppp) REVERT: E 402 MET cc_start: 0.7802 (mmm) cc_final: 0.6762 (ptm) REVERT: E 473 MET cc_start: 0.7844 (tpt) cc_final: 0.7518 (tpp) REVERT: E 488 LYS cc_start: 0.7936 (pttm) cc_final: 0.7242 (tppt) REVERT: E 500 TRP cc_start: 0.8193 (m100) cc_final: 0.7199 (m100) REVERT: E 599 PHE cc_start: 0.7899 (t80) cc_final: 0.6938 (t80) REVERT: F 300 PHE cc_start: 0.5392 (t80) cc_final: 0.5172 (t80) REVERT: F 302 ASP cc_start: 0.6428 (p0) cc_final: 0.5750 (p0) REVERT: F 369 MET cc_start: 0.5745 (mtp) cc_final: 0.4025 (tpp) REVERT: F 371 MET cc_start: 0.5987 (ppp) cc_final: 0.5762 (ppp) REVERT: F 623 ASN cc_start: 0.8141 (m-40) cc_final: 0.7824 (m-40) REVERT: F 639 TYR cc_start: 0.7972 (m-80) cc_final: 0.7715 (m-10) REVERT: F 740 MET cc_start: 0.8324 (ppp) cc_final: 0.8101 (ppp) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.4385 time to fit residues: 236.8563 Evaluate side-chains 238 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 188 optimal weight: 20.0000 chunk 241 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 329 optimal weight: 9.9990 chunk 206 optimal weight: 0.0070 chunk 200 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 overall best weight: 5.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 342 ASN B 602 GLN B 645 ASN B 684 ASN C 237 ASN ** C 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN ** C 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 ASN ** F 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.7454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27483 Z= 0.312 Angle : 0.685 9.621 37242 Z= 0.351 Chirality : 0.042 0.190 4219 Planarity : 0.006 0.101 4825 Dihedral : 11.210 89.607 4140 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.65 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.42 (0.15), residues: 3412 helix: 1.31 (0.12), residues: 1857 sheet: 0.67 (0.26), residues: 410 loop : -1.61 (0.20), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 219 HIS 0.008 0.002 HIS E 254 PHE 0.021 0.002 PHE B 476 TYR 0.025 0.002 TYR D 752 ARG 0.009 0.001 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 4.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.8137 (tpt) cc_final: 0.7757 (tpp) REVERT: A 517 ILE cc_start: 0.9069 (mp) cc_final: 0.8853 (mm) REVERT: A 616 ASP cc_start: 0.8124 (p0) cc_final: 0.7893 (p0) REVERT: A 638 ILE cc_start: 0.7042 (mp) cc_final: 0.6753 (mt) REVERT: A 740 MET cc_start: 0.8644 (tmm) cc_final: 0.8280 (tmm) REVERT: B 231 MET cc_start: 0.8767 (mtt) cc_final: 0.8511 (mtt) REVERT: B 292 ILE cc_start: 0.9471 (pt) cc_final: 0.9008 (mt) REVERT: B 318 MET cc_start: 0.7046 (mmm) cc_final: 0.6800 (mmm) REVERT: B 616 ASP cc_start: 0.8351 (p0) cc_final: 0.7360 (p0) REVERT: B 798 MET cc_start: 0.8136 (mmm) cc_final: 0.7694 (mmm) REVERT: C 231 MET cc_start: 0.8132 (ppp) cc_final: 0.6950 (tmm) REVERT: C 233 TYR cc_start: 0.7108 (m-10) cc_final: 0.5970 (m-80) REVERT: C 603 MET cc_start: 0.6361 (tpt) cc_final: 0.5998 (tpt) REVERT: C 740 MET cc_start: 0.9191 (tmm) cc_final: 0.8892 (tmm) REVERT: D 355 LEU cc_start: 0.8934 (mt) cc_final: 0.8604 (mt) REVERT: E 279 GLU cc_start: 0.8634 (tt0) cc_final: 0.7305 (tp30) REVERT: E 318 MET cc_start: 0.8343 (ppp) cc_final: 0.7963 (ppp) REVERT: E 361 ARG cc_start: 0.8765 (mmt180) cc_final: 0.8479 (mmm-85) REVERT: E 473 MET cc_start: 0.7939 (tpt) cc_final: 0.7624 (tpp) REVERT: E 514 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7050 (mt-10) REVERT: E 599 PHE cc_start: 0.8249 (t80) cc_final: 0.7201 (t80) REVERT: E 740 MET cc_start: 0.8848 (ppp) cc_final: 0.8510 (ppp) REVERT: F 215 LEU cc_start: 0.8306 (tp) cc_final: 0.8080 (tp) REVERT: F 300 PHE cc_start: 0.5918 (t80) cc_final: 0.5586 (t80) REVERT: F 302 ASP cc_start: 0.6502 (p0) cc_final: 0.5926 (p0) REVERT: F 369 MET cc_start: 0.5637 (mtp) cc_final: 0.4765 (mpp) REVERT: F 377 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7717 (ptp-170) REVERT: F 402 MET cc_start: 0.9220 (ptp) cc_final: 0.9016 (mpp) REVERT: F 452 ASP cc_start: 0.8585 (m-30) cc_final: 0.8304 (m-30) REVERT: F 525 GLU cc_start: 0.8491 (pm20) cc_final: 0.8261 (pm20) REVERT: F 623 ASN cc_start: 0.8386 (m-40) cc_final: 0.8169 (m-40) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.4018 time to fit residues: 197.5544 Evaluate side-chains 236 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 209 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN B 438 HIS ** C 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 ASN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.7783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27483 Z= 0.250 Angle : 0.635 11.290 37242 Z= 0.322 Chirality : 0.041 0.187 4219 Planarity : 0.006 0.098 4825 Dihedral : 10.881 88.966 4140 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.83 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.43 (0.15), residues: 3412 helix: 1.31 (0.12), residues: 1857 sheet: 0.53 (0.26), residues: 406 loop : -1.52 (0.20), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 219 HIS 0.009 0.001 HIS B 799 PHE 0.018 0.002 PHE D 476 TYR 0.023 0.002 TYR D 752 ARG 0.015 0.001 ARG C 489 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 VAL cc_start: 0.7872 (t) cc_final: 0.7583 (m) REVERT: A 473 MET cc_start: 0.8032 (tpt) cc_final: 0.7671 (tpp) REVERT: A 638 ILE cc_start: 0.7160 (mp) cc_final: 0.6906 (mt) REVERT: A 740 MET cc_start: 0.8647 (tmm) cc_final: 0.8272 (tmm) REVERT: A 798 MET cc_start: 0.7082 (tmm) cc_final: 0.6855 (tmm) REVERT: B 231 MET cc_start: 0.8983 (mtt) cc_final: 0.8667 (mtt) REVERT: B 292 ILE cc_start: 0.9430 (pt) cc_final: 0.9000 (mt) REVERT: B 318 MET cc_start: 0.7059 (mmm) cc_final: 0.6756 (mmm) REVERT: B 616 ASP cc_start: 0.8258 (p0) cc_final: 0.7318 (p0) REVERT: B 798 MET cc_start: 0.8193 (mmm) cc_final: 0.7799 (mmm) REVERT: C 740 MET cc_start: 0.9205 (tmm) cc_final: 0.8886 (tmm) REVERT: D 752 TYR cc_start: 0.7840 (m-80) cc_final: 0.7155 (m-80) REVERT: E 279 GLU cc_start: 0.8598 (tt0) cc_final: 0.7265 (tp30) REVERT: E 318 MET cc_start: 0.8197 (ppp) cc_final: 0.7832 (ppp) REVERT: E 361 ARG cc_start: 0.8759 (mmt180) cc_final: 0.8555 (mmm-85) REVERT: E 473 MET cc_start: 0.7960 (tpt) cc_final: 0.7631 (tpp) REVERT: E 599 PHE cc_start: 0.8110 (t80) cc_final: 0.7039 (t80) REVERT: E 740 MET cc_start: 0.8871 (ppp) cc_final: 0.8523 (ppp) REVERT: F 235 TYR cc_start: 0.4350 (p90) cc_final: 0.4047 (p90) REVERT: F 302 ASP cc_start: 0.6477 (p0) cc_final: 0.5674 (p0) REVERT: F 369 MET cc_start: 0.5568 (mtp) cc_final: 0.4804 (mpp) REVERT: F 377 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7778 (ptp-170) REVERT: F 402 MET cc_start: 0.9210 (ptp) cc_final: 0.8986 (mpp) REVERT: F 452 ASP cc_start: 0.8520 (m-30) cc_final: 0.8247 (m-30) REVERT: F 525 GLU cc_start: 0.8326 (pm20) cc_final: 0.8053 (pm20) REVERT: F 623 ASN cc_start: 0.8375 (m-40) cc_final: 0.8079 (m-40) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.3968 time to fit residues: 200.7024 Evaluate side-chains 231 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 10.0000 chunk 315 optimal weight: 9.9990 chunk 288 optimal weight: 5.9990 chunk 307 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 241 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 277 optimal weight: 20.0000 chunk 290 optimal weight: 6.9990 chunk 306 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 ASN C 785 ASN D 342 ASN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.8279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27483 Z= 0.361 Angle : 0.734 14.380 37242 Z= 0.376 Chirality : 0.043 0.208 4219 Planarity : 0.006 0.104 4825 Dihedral : 10.923 83.057 4140 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.39 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.04 (0.15), residues: 3412 helix: 0.89 (0.12), residues: 1869 sheet: 0.38 (0.25), residues: 403 loop : -1.71 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 453 HIS 0.010 0.002 HIS E 254 PHE 0.029 0.002 PHE B 476 TYR 0.027 0.002 TYR C 752 ARG 0.007 0.001 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 3.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.8101 (tpt) cc_final: 0.7750 (tpp) REVERT: A 795 GLU cc_start: 0.7888 (mp0) cc_final: 0.7623 (mp0) REVERT: A 798 MET cc_start: 0.7197 (tmm) cc_final: 0.6994 (tmm) REVERT: B 231 MET cc_start: 0.8867 (mtt) cc_final: 0.8515 (mtt) REVERT: B 292 ILE cc_start: 0.9463 (pt) cc_final: 0.9040 (mt) REVERT: B 527 PHE cc_start: 0.7569 (m-80) cc_final: 0.7169 (m-80) REVERT: B 616 ASP cc_start: 0.8130 (p0) cc_final: 0.7114 (p0) REVERT: B 798 MET cc_start: 0.8184 (mmm) cc_final: 0.7783 (mmm) REVERT: C 489 ARG cc_start: 0.7466 (ptp-170) cc_final: 0.6924 (ptp-170) REVERT: C 740 MET cc_start: 0.9213 (tmm) cc_final: 0.8898 (tmm) REVERT: D 752 TYR cc_start: 0.7987 (m-80) cc_final: 0.7182 (m-80) REVERT: E 279 GLU cc_start: 0.8769 (tt0) cc_final: 0.7453 (tp30) REVERT: E 318 MET cc_start: 0.8265 (ppp) cc_final: 0.7826 (ppp) REVERT: E 473 MET cc_start: 0.7941 (tpt) cc_final: 0.7692 (tpp) REVERT: E 599 PHE cc_start: 0.8232 (t80) cc_final: 0.7287 (t80) REVERT: E 740 MET cc_start: 0.8892 (ppp) cc_final: 0.8540 (ppp) REVERT: F 215 LEU cc_start: 0.8489 (tp) cc_final: 0.8143 (tp) REVERT: F 235 TYR cc_start: 0.4461 (p90) cc_final: 0.4043 (p90) REVERT: F 300 PHE cc_start: 0.6108 (t80) cc_final: 0.5777 (t80) REVERT: F 302 ASP cc_start: 0.6524 (p0) cc_final: 0.5836 (p0) REVERT: F 330 MET cc_start: 0.5553 (ttt) cc_final: 0.5268 (ttt) REVERT: F 346 LEU cc_start: 0.9319 (tp) cc_final: 0.9110 (tp) REVERT: F 369 MET cc_start: 0.5754 (mtp) cc_final: 0.4772 (mpp) REVERT: F 377 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.6908 (ptp90) REVERT: F 402 MET cc_start: 0.9235 (ptp) cc_final: 0.8974 (mpp) REVERT: F 452 ASP cc_start: 0.8607 (m-30) cc_final: 0.8332 (m-30) REVERT: F 525 GLU cc_start: 0.8401 (pm20) cc_final: 0.8136 (pm20) REVERT: F 567 LYS cc_start: 0.7699 (tptp) cc_final: 0.7429 (tppt) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.3935 time to fit residues: 183.6820 Evaluate side-chains 226 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 3.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 8.9990 chunk 324 optimal weight: 0.0980 chunk 198 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 chunk 340 optimal weight: 30.0000 chunk 313 optimal weight: 8.9990 chunk 271 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 557 ASN ** F 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.8562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27483 Z= 0.283 Angle : 0.670 9.996 37242 Z= 0.341 Chirality : 0.042 0.178 4219 Planarity : 0.006 0.100 4825 Dihedral : 10.581 84.779 4140 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.18 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.11 (0.15), residues: 3412 helix: 0.96 (0.12), residues: 1880 sheet: 0.36 (0.26), residues: 398 loop : -1.50 (0.20), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 219 HIS 0.010 0.001 HIS E 254 PHE 0.018 0.002 PHE F 354 TYR 0.023 0.002 TYR C 752 ARG 0.007 0.001 ARG C 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ARG cc_start: 0.5929 (tpt170) cc_final: 0.5724 (tpt170) REVERT: A 473 MET cc_start: 0.7962 (tpt) cc_final: 0.7627 (tpp) REVERT: A 603 MET cc_start: 0.8729 (mmp) cc_final: 0.8355 (mmp) REVERT: A 795 GLU cc_start: 0.8105 (mp0) cc_final: 0.7800 (mp0) REVERT: A 798 MET cc_start: 0.7359 (tmm) cc_final: 0.7097 (tmm) REVERT: B 231 MET cc_start: 0.8709 (mtt) cc_final: 0.8414 (mtt) REVERT: B 292 ILE cc_start: 0.9466 (pt) cc_final: 0.9030 (mt) REVERT: B 527 PHE cc_start: 0.7616 (m-80) cc_final: 0.7212 (m-80) REVERT: B 616 ASP cc_start: 0.8205 (p0) cc_final: 0.7307 (p0) REVERT: B 798 MET cc_start: 0.8172 (mmm) cc_final: 0.7811 (mmm) REVERT: C 350 ASN cc_start: 0.8632 (m-40) cc_final: 0.8314 (m-40) REVERT: C 489 ARG cc_start: 0.7223 (ptp-170) cc_final: 0.6302 (ptm160) REVERT: C 603 MET cc_start: 0.7778 (mmm) cc_final: 0.7549 (tpp) REVERT: C 740 MET cc_start: 0.9224 (tmm) cc_final: 0.8927 (tmm) REVERT: D 752 TYR cc_start: 0.7565 (m-80) cc_final: 0.6919 (m-80) REVERT: E 279 GLU cc_start: 0.8730 (tt0) cc_final: 0.7475 (tp30) REVERT: E 318 MET cc_start: 0.7958 (ppp) cc_final: 0.7687 (ppp) REVERT: E 325 GLU cc_start: 0.7958 (tp30) cc_final: 0.7742 (tp30) REVERT: E 473 MET cc_start: 0.7916 (tpt) cc_final: 0.7574 (tpp) REVERT: E 599 PHE cc_start: 0.8104 (t80) cc_final: 0.7203 (t80) REVERT: E 740 MET cc_start: 0.8853 (ppp) cc_final: 0.8477 (ppp) REVERT: F 215 LEU cc_start: 0.8452 (tp) cc_final: 0.8086 (tp) REVERT: F 235 TYR cc_start: 0.4348 (p90) cc_final: 0.4033 (p90) REVERT: F 300 PHE cc_start: 0.5946 (t80) cc_final: 0.5628 (t80) REVERT: F 302 ASP cc_start: 0.6571 (p0) cc_final: 0.5988 (p0) REVERT: F 369 MET cc_start: 0.5787 (mtp) cc_final: 0.4446 (mpp) REVERT: F 371 MET cc_start: 0.5690 (ppp) cc_final: 0.5349 (ppp) REVERT: F 402 MET cc_start: 0.9197 (ptp) cc_final: 0.8989 (mpp) REVERT: F 452 ASP cc_start: 0.8630 (m-30) cc_final: 0.8369 (m-30) REVERT: F 525 GLU cc_start: 0.8481 (pm20) cc_final: 0.8227 (pm20) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.4092 time to fit residues: 194.6462 Evaluate side-chains 222 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 9.9990 chunk 289 optimal weight: 30.0000 chunk 83 optimal weight: 8.9990 chunk 250 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 279 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 GLN ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 ASN ** C 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 ASN ** F 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.080608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.067022 restraints weight = 125374.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.068443 restraints weight = 88356.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.069368 restraints weight = 66909.960| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.8675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27483 Z= 0.213 Angle : 0.635 13.157 37242 Z= 0.320 Chirality : 0.042 0.185 4219 Planarity : 0.005 0.093 4825 Dihedral : 10.297 86.485 4140 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.57 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.27 (0.15), residues: 3412 helix: 1.08 (0.12), residues: 1882 sheet: 0.41 (0.26), residues: 399 loop : -1.41 (0.20), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 219 HIS 0.009 0.001 HIS E 254 PHE 0.016 0.002 PHE F 354 TYR 0.021 0.002 TYR D 752 ARG 0.006 0.001 ARG F 610 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5511.79 seconds wall clock time: 101 minutes 26.64 seconds (6086.64 seconds total)