Starting phenix.real_space_refine on Wed Mar 20 22:01:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rk6_24493/03_2024/7rk6_24493_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rk6_24493/03_2024/7rk6_24493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rk6_24493/03_2024/7rk6_24493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rk6_24493/03_2024/7rk6_24493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rk6_24493/03_2024/7rk6_24493_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rk6_24493/03_2024/7rk6_24493_updated.pdb" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians Ba 8 18.26 5 K 3 8.98 5 P 4 5.49 5 S 168 5.16 5 C 18548 2.51 5 N 4700 2.21 5 O 5184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28615 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 7104 Classifications: {'peptide': 891} Link IDs: {'PTRANS': 35, 'TRANS': 855} Chain breaks: 4 Chain: "B" Number of atoms: 7104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 7104 Classifications: {'peptide': 891} Link IDs: {'PTRANS': 35, 'TRANS': 855} Chain breaks: 4 Chain: "C" Number of atoms: 7104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 7104 Classifications: {'peptide': 891} Link IDs: {'PTRANS': 35, 'TRANS': 855} Chain breaks: 4 Chain: "D" Number of atoms: 7104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 7104 Classifications: {'peptide': 891} Link IDs: {'PTRANS': 35, 'TRANS': 855} Chain breaks: 4 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 51 Unusual residues: {' K': 3, ' BA': 2, 'PGW': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {' BA': 2, 'PGW': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {' BA': 2, 'PGW': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {' BA': 2, 'PGW': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 14.87, per 1000 atoms: 0.52 Number of scatterers: 28615 At special positions: 0 Unit cell: (171.57, 171.57, 125.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ba 8 55.98 K 3 19.00 S 168 16.00 P 4 15.00 O 5184 8.00 N 4700 7.00 C 18548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 606 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 606 " - pdb=" SG CYS D 619 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.11 Conformation dependent library (CDL) restraints added in 5.3 seconds 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 180 helices and 16 sheets defined 47.6% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.21 Creating SS restraints... Processing helix chain 'A' and resid 20 through 42 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 97 through 122 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 179 through 188 Processing helix chain 'A' and resid 196 through 213 Proline residue: A 207 - end of helix removed outlier: 3.605A pdb=" N LEU A 210 " --> pdb=" O PRO A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 248 Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 287 through 316 Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 342 through 352 removed outlier: 4.229A pdb=" N ASN A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 422 through 439 Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 492 through 499 removed outlier: 3.524A pdb=" N MET A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 removed outlier: 3.559A pdb=" N GLY A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 593 through 601 removed outlier: 3.971A pdb=" N ARG A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 762 through 764 No H-bonds generated for 'chain 'A' and resid 762 through 764' Processing helix chain 'A' and resid 770 through 772 No H-bonds generated for 'chain 'A' and resid 770 through 772' Processing helix chain 'A' and resid 782 through 794 removed outlier: 4.258A pdb=" N LYS A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N THR A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASN A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 813 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 840 through 850 Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.856A pdb=" N GLN A 899 " --> pdb=" O SER A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 921 Processing helix chain 'A' and resid 927 through 939 removed outlier: 3.889A pdb=" N THR A 936 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER A 937 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 951 Processing helix chain 'A' and resid 957 through 965 Processing helix chain 'A' and resid 978 through 982 removed outlier: 3.728A pdb=" N ASN A 981 " --> pdb=" O VAL A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1001 Processing helix chain 'A' and resid 1006 through 1017 Processing helix chain 'B' and resid 20 through 42 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 97 through 122 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 179 through 188 Processing helix chain 'B' and resid 196 through 213 Proline residue: B 207 - end of helix removed outlier: 3.604A pdb=" N LEU B 210 " --> pdb=" O PRO B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 248 Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 287 through 316 Proline residue: B 309 - end of helix Processing helix chain 'B' and resid 342 through 352 removed outlier: 4.229A pdb=" N ASN B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 382 Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 422 through 439 Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 457 through 460 Processing helix chain 'B' and resid 466 through 468 No H-bonds generated for 'chain 'B' and resid 466 through 468' Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 492 through 499 removed outlier: 3.523A pdb=" N MET B 496 " --> pdb=" O PHE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 522 removed outlier: 3.559A pdb=" N GLY B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 540 through 549 Processing helix chain 'B' and resid 561 through 563 No H-bonds generated for 'chain 'B' and resid 561 through 563' Processing helix chain 'B' and resid 593 through 601 removed outlier: 3.972A pdb=" N ARG B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR B 601 " --> pdb=" O LYS B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 722 through 724 No H-bonds generated for 'chain 'B' and resid 722 through 724' Processing helix chain 'B' and resid 729 through 734 Processing helix chain 'B' and resid 756 through 760 Processing helix chain 'B' and resid 762 through 764 No H-bonds generated for 'chain 'B' and resid 762 through 764' Processing helix chain 'B' and resid 770 through 772 No H-bonds generated for 'chain 'B' and resid 770 through 772' Processing helix chain 'B' and resid 782 through 794 removed outlier: 4.258A pdb=" N LYS B 790 " --> pdb=" O HIS B 786 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASN B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 835 through 837 No H-bonds generated for 'chain 'B' and resid 835 through 837' Processing helix chain 'B' and resid 840 through 850 Processing helix chain 'B' and resid 895 through 901 removed outlier: 3.857A pdb=" N GLN B 899 " --> pdb=" O SER B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 921 Processing helix chain 'B' and resid 927 through 939 removed outlier: 3.890A pdb=" N THR B 936 " --> pdb=" O LEU B 933 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER B 937 " --> pdb=" O MET B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 951 Processing helix chain 'B' and resid 957 through 965 Processing helix chain 'B' and resid 978 through 982 removed outlier: 3.727A pdb=" N ASN B 981 " --> pdb=" O VAL B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1001 Processing helix chain 'B' and resid 1006 through 1017 Processing helix chain 'C' and resid 20 through 42 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 97 through 122 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 179 through 188 Processing helix chain 'C' and resid 196 through 213 Proline residue: C 207 - end of helix removed outlier: 3.605A pdb=" N LEU C 210 " --> pdb=" O PRO C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 248 Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 287 through 316 Proline residue: C 309 - end of helix Processing helix chain 'C' and resid 342 through 352 removed outlier: 4.230A pdb=" N ASN C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 382 Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 422 through 439 Processing helix chain 'C' and resid 453 through 455 No H-bonds generated for 'chain 'C' and resid 453 through 455' Processing helix chain 'C' and resid 457 through 460 Processing helix chain 'C' and resid 466 through 468 No H-bonds generated for 'chain 'C' and resid 466 through 468' Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 492 through 499 removed outlier: 3.524A pdb=" N MET C 496 " --> pdb=" O PHE C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 522 removed outlier: 3.559A pdb=" N GLY C 521 " --> pdb=" O ASP C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 535 No H-bonds generated for 'chain 'C' and resid 533 through 535' Processing helix chain 'C' and resid 540 through 549 Processing helix chain 'C' and resid 561 through 563 No H-bonds generated for 'chain 'C' and resid 561 through 563' Processing helix chain 'C' and resid 593 through 601 removed outlier: 3.971A pdb=" N ARG C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE C 600 " --> pdb=" O VAL C 596 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR C 601 " --> pdb=" O LYS C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 722 through 724 No H-bonds generated for 'chain 'C' and resid 722 through 724' Processing helix chain 'C' and resid 729 through 734 Processing helix chain 'C' and resid 756 through 760 Processing helix chain 'C' and resid 762 through 764 No H-bonds generated for 'chain 'C' and resid 762 through 764' Processing helix chain 'C' and resid 770 through 772 No H-bonds generated for 'chain 'C' and resid 770 through 772' Processing helix chain 'C' and resid 782 through 794 removed outlier: 4.258A pdb=" N LYS C 790 " --> pdb=" O HIS C 786 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N THR C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASN C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 813 Processing helix chain 'C' and resid 835 through 837 No H-bonds generated for 'chain 'C' and resid 835 through 837' Processing helix chain 'C' and resid 840 through 850 Processing helix chain 'C' and resid 895 through 901 removed outlier: 3.856A pdb=" N GLN C 899 " --> pdb=" O SER C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 921 Processing helix chain 'C' and resid 927 through 939 removed outlier: 3.890A pdb=" N THR C 936 " --> pdb=" O LEU C 933 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER C 937 " --> pdb=" O MET C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 951 Processing helix chain 'C' and resid 957 through 965 Processing helix chain 'C' and resid 978 through 982 removed outlier: 3.727A pdb=" N ASN C 981 " --> pdb=" O VAL C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1001 Processing helix chain 'C' and resid 1006 through 1017 Processing helix chain 'D' and resid 20 through 42 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 97 through 122 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 179 through 188 Processing helix chain 'D' and resid 196 through 213 Proline residue: D 207 - end of helix removed outlier: 3.605A pdb=" N LEU D 210 " --> pdb=" O PRO D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 248 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 263 through 274 Processing helix chain 'D' and resid 287 through 316 Proline residue: D 309 - end of helix Processing helix chain 'D' and resid 342 through 352 removed outlier: 4.229A pdb=" N ASN D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 382 Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 422 through 439 Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 457 through 460 Processing helix chain 'D' and resid 466 through 468 No H-bonds generated for 'chain 'D' and resid 466 through 468' Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 492 through 499 removed outlier: 3.524A pdb=" N MET D 496 " --> pdb=" O PHE D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 522 removed outlier: 3.559A pdb=" N GLY D 521 " --> pdb=" O ASP D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 540 through 549 Processing helix chain 'D' and resid 561 through 563 No H-bonds generated for 'chain 'D' and resid 561 through 563' Processing helix chain 'D' and resid 593 through 601 removed outlier: 3.971A pdb=" N ARG D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR D 601 " --> pdb=" O LYS D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 615 No H-bonds generated for 'chain 'D' and resid 613 through 615' Processing helix chain 'D' and resid 722 through 724 No H-bonds generated for 'chain 'D' and resid 722 through 724' Processing helix chain 'D' and resid 729 through 734 Processing helix chain 'D' and resid 756 through 760 Processing helix chain 'D' and resid 762 through 764 No H-bonds generated for 'chain 'D' and resid 762 through 764' Processing helix chain 'D' and resid 770 through 772 No H-bonds generated for 'chain 'D' and resid 770 through 772' Processing helix chain 'D' and resid 782 through 794 removed outlier: 4.258A pdb=" N LYS D 790 " --> pdb=" O HIS D 786 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N THR D 791 " --> pdb=" O ARG D 787 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASN D 794 " --> pdb=" O LYS D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 813 Processing helix chain 'D' and resid 835 through 837 No H-bonds generated for 'chain 'D' and resid 835 through 837' Processing helix chain 'D' and resid 840 through 850 Processing helix chain 'D' and resid 895 through 901 removed outlier: 3.856A pdb=" N GLN D 899 " --> pdb=" O SER D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 917 through 921 Processing helix chain 'D' and resid 927 through 939 removed outlier: 3.889A pdb=" N THR D 936 " --> pdb=" O LEU D 933 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER D 937 " --> pdb=" O MET D 934 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 951 Processing helix chain 'D' and resid 957 through 965 Processing helix chain 'D' and resid 978 through 982 removed outlier: 3.728A pdb=" N ASN D 981 " --> pdb=" O VAL D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1001 Processing helix chain 'D' and resid 1006 through 1017 Processing sheet with id= A, first strand: chain 'A' and resid 362 through 367 removed outlier: 7.305A pdb=" N ARG A 332 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL A 365 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 334 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU A 367 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 336 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA A 410 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N CYS A 337 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A 412 " --> pdb=" O CYS A 337 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS A 444 " --> pdb=" O CYS A 411 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL A 413 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE A 446 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP A 471 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU A 449 " --> pdb=" O ASP A 471 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 473 " --> pdb=" O LEU A 449 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 525 through 530 removed outlier: 4.533A pdb=" N GLN A 585 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 557 " --> pdb=" O PHE A 587 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE A 589 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU A 555 " --> pdb=" O ILE A 589 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 924 through 926 removed outlier: 7.962A pdb=" N PHE A 925 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR A 890 " --> pdb=" O PHE A 925 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS A 822 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLU A 891 " --> pdb=" O CYS A 822 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE A 824 " --> pdb=" O GLU A 891 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N SER A 799 " --> pdb=" O ILE A 778 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLY A 780 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A 801 " --> pdb=" O GLY A 780 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 988 through 991 removed outlier: 3.742A pdb=" N GLY A1023 " --> pdb=" O TYR A1060 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 362 through 367 removed outlier: 7.305A pdb=" N ARG B 332 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL B 365 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL B 334 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU B 367 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 336 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA B 410 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N CYS B 337 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B 412 " --> pdb=" O CYS B 337 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS B 444 " --> pdb=" O CYS B 411 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL B 413 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE B 446 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP B 471 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU B 449 " --> pdb=" O ASP B 471 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL B 473 " --> pdb=" O LEU B 449 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 525 through 530 removed outlier: 4.532A pdb=" N GLN B 585 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 557 " --> pdb=" O PHE B 587 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE B 589 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU B 555 " --> pdb=" O ILE B 589 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 924 through 926 removed outlier: 7.963A pdb=" N PHE B 925 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR B 890 " --> pdb=" O PHE B 925 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS B 822 " --> pdb=" O ILE B 889 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLU B 891 " --> pdb=" O CYS B 822 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE B 824 " --> pdb=" O GLU B 891 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N SER B 799 " --> pdb=" O ILE B 778 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLY B 780 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU B 801 " --> pdb=" O GLY B 780 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 988 through 991 removed outlier: 3.742A pdb=" N GLY B1023 " --> pdb=" O TYR B1060 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 362 through 367 removed outlier: 7.304A pdb=" N ARG C 332 " --> pdb=" O GLU C 363 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL C 365 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL C 334 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU C 367 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL C 336 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 410 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N CYS C 337 " --> pdb=" O ALA C 410 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU C 412 " --> pdb=" O CYS C 337 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS C 444 " --> pdb=" O CYS C 411 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL C 413 " --> pdb=" O LYS C 444 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE C 446 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP C 471 " --> pdb=" O VAL C 447 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU C 449 " --> pdb=" O ASP C 471 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL C 473 " --> pdb=" O LEU C 449 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 525 through 530 removed outlier: 4.533A pdb=" N GLN C 585 " --> pdb=" O GLU C 559 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 557 " --> pdb=" O PHE C 587 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE C 589 " --> pdb=" O LEU C 555 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU C 555 " --> pdb=" O ILE C 589 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 924 through 926 removed outlier: 7.962A pdb=" N PHE C 925 " --> pdb=" O LEU C 888 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR C 890 " --> pdb=" O PHE C 925 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS C 822 " --> pdb=" O ILE C 889 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLU C 891 " --> pdb=" O CYS C 822 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 824 " --> pdb=" O GLU C 891 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N SER C 799 " --> pdb=" O ILE C 778 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLY C 780 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU C 801 " --> pdb=" O GLY C 780 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 988 through 991 removed outlier: 3.742A pdb=" N GLY C1023 " --> pdb=" O TYR C1060 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 362 through 367 removed outlier: 7.305A pdb=" N ARG D 332 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL D 365 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL D 334 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU D 367 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL D 336 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA D 410 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N CYS D 337 " --> pdb=" O ALA D 410 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU D 412 " --> pdb=" O CYS D 337 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS D 444 " --> pdb=" O CYS D 411 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL D 413 " --> pdb=" O LYS D 444 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE D 446 " --> pdb=" O VAL D 413 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP D 471 " --> pdb=" O VAL D 447 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU D 449 " --> pdb=" O ASP D 471 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL D 473 " --> pdb=" O LEU D 449 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 525 through 530 removed outlier: 4.533A pdb=" N GLN D 585 " --> pdb=" O GLU D 559 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 557 " --> pdb=" O PHE D 587 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE D 589 " --> pdb=" O LEU D 555 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU D 555 " --> pdb=" O ILE D 589 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 924 through 926 removed outlier: 7.962A pdb=" N PHE D 925 " --> pdb=" O LEU D 888 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR D 890 " --> pdb=" O PHE D 925 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS D 822 " --> pdb=" O ILE D 889 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLU D 891 " --> pdb=" O CYS D 822 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE D 824 " --> pdb=" O GLU D 891 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N SER D 799 " --> pdb=" O ILE D 778 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLY D 780 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU D 801 " --> pdb=" O GLY D 780 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 988 through 991 removed outlier: 3.742A pdb=" N GLY D1023 " --> pdb=" O TYR D1060 " (cutoff:3.500A) 1084 hydrogen bonds defined for protein. 2892 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: 10.73 Time building geometry restraints manager: 12.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5857 1.33 - 1.45: 6906 1.45 - 1.57: 16229 1.57 - 1.69: 4 1.69 - 1.81: 260 Bond restraints: 29256 Sorted by residual: bond pdb=" C10 PGW A1105 " pdb=" C9 PGW A1105 " ideal model delta sigma weight residual 1.333 1.553 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C10 PGW D1105 " pdb=" C9 PGW D1105 " ideal model delta sigma weight residual 1.333 1.553 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C10 PGW B1105 " pdb=" C9 PGW B1105 " ideal model delta sigma weight residual 1.333 1.553 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C10 PGW C1105 " pdb=" C9 PGW C1105 " ideal model delta sigma weight residual 1.333 1.553 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" O14 PGW B1106 " pdb=" P PGW B1106 " ideal model delta sigma weight residual 1.512 1.731 -0.219 2.00e-02 2.50e+03 1.19e+02 ... (remaining 29251 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.19: 518 105.19 - 112.39: 14552 112.39 - 119.59: 9802 119.59 - 126.79: 14385 126.79 - 133.98: 387 Bond angle restraints: 39644 Sorted by residual: angle pdb=" O12 PGW B1106 " pdb=" P PGW B1106 " pdb=" O13 PGW B1106 " ideal model delta sigma weight residual 111.13 127.01 -15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" O12 PGW C1106 " pdb=" P PGW C1106 " pdb=" O13 PGW C1106 " ideal model delta sigma weight residual 111.13 126.96 -15.83 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O12 PGW A1106 " pdb=" P PGW A1106 " pdb=" O13 PGW A1106 " ideal model delta sigma weight residual 111.13 126.96 -15.83 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O12 PGW D1106 " pdb=" P PGW D1106 " pdb=" O13 PGW D1106 " ideal model delta sigma weight residual 111.13 126.96 -15.83 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O13 PGW B1106 " pdb=" P PGW B1106 " pdb=" O14 PGW B1106 " ideal model delta sigma weight residual 119.81 104.03 15.78 3.00e+00 1.11e-01 2.77e+01 ... (remaining 39639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 15454 16.79 - 33.57: 1480 33.57 - 50.35: 310 50.35 - 67.14: 56 67.14 - 83.92: 24 Dihedral angle restraints: 17324 sinusoidal: 6916 harmonic: 10408 Sorted by residual: dihedral pdb=" CB CYS B 606 " pdb=" SG CYS B 606 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual -86.00 -152.09 66.09 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS C 606 " pdb=" SG CYS C 606 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual -86.00 -152.03 66.03 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" CB CYS A 606 " pdb=" SG CYS A 606 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual -86.00 -152.02 66.02 1 1.00e+01 1.00e-02 5.70e+01 ... (remaining 17321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2543 0.028 - 0.055: 1154 0.055 - 0.083: 486 0.083 - 0.111: 235 0.111 - 0.139: 38 Chirality restraints: 4456 Sorted by residual: chirality pdb=" CA ILE C 572 " pdb=" N ILE C 572 " pdb=" C ILE C 572 " pdb=" CB ILE C 572 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE B 572 " pdb=" N ILE B 572 " pdb=" C ILE B 572 " pdb=" CB ILE B 572 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE A 572 " pdb=" N ILE A 572 " pdb=" C ILE A 572 " pdb=" CB ILE A 572 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 4453 not shown) Planarity restraints: 5020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW B1105 " -0.039 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C10 PGW B1105 " 0.039 2.00e-02 2.50e+03 pdb=" C8 PGW B1105 " -0.039 2.00e-02 2.50e+03 pdb=" C9 PGW B1105 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A1105 " -0.039 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C10 PGW A1105 " 0.038 2.00e-02 2.50e+03 pdb=" C8 PGW A1105 " -0.039 2.00e-02 2.50e+03 pdb=" C9 PGW A1105 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW C1105 " 0.039 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C10 PGW C1105 " -0.038 2.00e-02 2.50e+03 pdb=" C8 PGW C1105 " 0.039 2.00e-02 2.50e+03 pdb=" C9 PGW C1105 " -0.039 2.00e-02 2.50e+03 ... (remaining 5017 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 7987 2.80 - 3.39: 33670 3.39 - 3.97: 55894 3.97 - 4.56: 80876 4.56 - 5.14: 115157 Nonbonded interactions: 293584 Sorted by model distance: nonbonded pdb=" O VAL B 929 " pdb=" OG SER B 932 " model vdw 2.216 2.440 nonbonded pdb=" O VAL D 929 " pdb=" OG SER D 932 " model vdw 2.216 2.440 nonbonded pdb=" O VAL A 929 " pdb=" OG SER A 932 " model vdw 2.216 2.440 nonbonded pdb=" O VAL C 929 " pdb=" OG SER C 932 " model vdw 2.217 2.440 nonbonded pdb=" O LEU A 551 " pdb=" NH2 ARG A 598 " model vdw 2.222 2.520 ... (remaining 293579 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 15 through 1066 or resid 1101 through 1106)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 5.160 Check model and map are aligned: 0.580 Set scattering table: 0.330 Process input model: 78.780 Find NCS groups from input model: 1.940 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: 0.000 Load rotamer database and sin/cos tables:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 : 0.005 0.220 29256 Z= 0.350 Angle : 0.631 15.879 39644 Z= 0.302 Chirality : 0.041 0.139 4456 Planarity : 0.003 0.041 5020 Dihedral : 13.959 83.925 10584 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3524 helix: 0.51 (0.13), residues: 1688 sheet: -2.48 (0.26), residues: 384 loop : -0.16 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 789 HIS 0.003 0.001 HIS B 354 PHE 0.031 0.001 PHE D 118 TYR 0.012 0.001 TYR C1064 ARG 0.004 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 3.496 Fit side-chains REVERT: A 145 PHE cc_start: 0.8094 (m-10) cc_final: 0.7877 (m-80) REVERT: A 298 MET cc_start: 0.8556 (mpp) cc_final: 0.8255 (mpp) REVERT: A 300 PHE cc_start: 0.8867 (t80) cc_final: 0.8501 (t80) REVERT: A 420 GLN cc_start: 0.7870 (mp10) cc_final: 0.7594 (tp40) REVERT: B 298 MET cc_start: 0.8562 (mpp) cc_final: 0.8259 (mpp) REVERT: B 300 PHE cc_start: 0.8869 (t80) cc_final: 0.8505 (t80) REVERT: B 420 GLN cc_start: 0.7874 (mp10) cc_final: 0.7597 (tp40) REVERT: C 145 PHE cc_start: 0.8089 (m-10) cc_final: 0.7869 (m-80) REVERT: C 298 MET cc_start: 0.8557 (mpp) cc_final: 0.8261 (mpp) REVERT: C 300 PHE cc_start: 0.8869 (t80) cc_final: 0.8503 (t80) REVERT: C 420 GLN cc_start: 0.7868 (mp10) cc_final: 0.7591 (tp40) REVERT: D 298 MET cc_start: 0.8556 (mpp) cc_final: 0.8259 (mpp) REVERT: D 300 PHE cc_start: 0.8866 (t80) cc_final: 0.8501 (t80) REVERT: D 420 GLN cc_start: 0.7867 (mp10) cc_final: 0.7591 (tp40) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 1.1416 time to fit residues: 383.4337 Evaluate side-chains 215 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 0.0570 chunk 269 optimal weight: 40.0000 chunk 149 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 182 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 279 optimal weight: 0.7980 chunk 107 optimal weight: 20.0000 chunk 169 optimal weight: 0.0060 chunk 207 optimal weight: 1.9990 chunk 323 optimal weight: 0.8980 overall best weight: 0.7516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 406 GLN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN A 454 ASN B 347 ASN B 406 GLN B 448 GLN B 454 ASN C 406 GLN ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN C 454 ASN D 347 ASN D 406 GLN D 448 GLN D 454 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 29256 Z= 0.170 Angle : 0.509 7.963 39644 Z= 0.253 Chirality : 0.040 0.136 4456 Planarity : 0.003 0.039 5020 Dihedral : 7.494 85.466 3972 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.03 % Allowed : 7.24 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 3524 helix: 0.66 (0.13), residues: 1696 sheet: -2.34 (0.26), residues: 376 loop : -0.08 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 235 HIS 0.003 0.001 HIS A 354 PHE 0.019 0.001 PHE B 296 TYR 0.017 0.001 TYR B 268 ARG 0.006 0.000 ARG B 614 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 261 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 PHE cc_start: 0.9359 (m-80) cc_final: 0.8798 (m-80) REVERT: A 268 TYR cc_start: 0.8654 (t80) cc_final: 0.8406 (t80) REVERT: A 298 MET cc_start: 0.8358 (mpp) cc_final: 0.8155 (mpp) REVERT: A 901 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8731 (mm) REVERT: B 154 PHE cc_start: 0.9359 (m-80) cc_final: 0.8799 (m-80) REVERT: B 268 TYR cc_start: 0.8654 (t80) cc_final: 0.8406 (t80) REVERT: B 298 MET cc_start: 0.8364 (mpp) cc_final: 0.8152 (mpp) REVERT: B 901 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8731 (mm) REVERT: C 154 PHE cc_start: 0.9359 (m-80) cc_final: 0.8798 (m-80) REVERT: C 268 TYR cc_start: 0.8657 (t80) cc_final: 0.8397 (t80) REVERT: C 298 MET cc_start: 0.8359 (mpp) cc_final: 0.8152 (mpp) REVERT: C 420 GLN cc_start: 0.7848 (mp10) cc_final: 0.7648 (tp40) REVERT: C 901 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8733 (mm) REVERT: D 154 PHE cc_start: 0.9360 (m-80) cc_final: 0.8799 (m-80) REVERT: D 268 TYR cc_start: 0.8651 (t80) cc_final: 0.8393 (t80) REVERT: D 298 MET cc_start: 0.8362 (mpp) cc_final: 0.8161 (mpp) REVERT: D 901 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8732 (mm) outliers start: 32 outliers final: 20 residues processed: 277 average time/residue: 1.0361 time to fit residues: 353.5004 Evaluate side-chains 258 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 234 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 941 ASP Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 895 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 941 ASP Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 269 optimal weight: 50.0000 chunk 220 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 323 optimal weight: 0.9990 chunk 349 optimal weight: 0.9980 chunk 288 optimal weight: 2.9990 chunk 321 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 259 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 448 GLN C 448 GLN D 448 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 29256 Z= 0.242 Angle : 0.534 7.854 39644 Z= 0.262 Chirality : 0.041 0.136 4456 Planarity : 0.003 0.037 5020 Dihedral : 7.160 84.386 3972 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.29 % Allowed : 9.49 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3524 helix: 0.53 (0.13), residues: 1736 sheet: -2.25 (0.27), residues: 376 loop : -0.02 (0.18), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 235 HIS 0.003 0.001 HIS D 333 PHE 0.023 0.001 PHE B 296 TYR 0.013 0.001 TYR D 268 ARG 0.004 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 259 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 PHE cc_start: 0.9384 (m-80) cc_final: 0.8760 (m-80) REVERT: A 268 TYR cc_start: 0.8700 (t80) cc_final: 0.8483 (t80) REVERT: A 298 MET cc_start: 0.8378 (mpp) cc_final: 0.8149 (mpp) REVERT: A 420 GLN cc_start: 0.7744 (tp40) cc_final: 0.7533 (tp40) REVERT: A 901 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8760 (mm) REVERT: B 154 PHE cc_start: 0.9383 (m-80) cc_final: 0.8762 (m-80) REVERT: B 268 TYR cc_start: 0.8694 (t80) cc_final: 0.8478 (t80) REVERT: B 298 MET cc_start: 0.8384 (mpp) cc_final: 0.8145 (mpp) REVERT: B 420 GLN cc_start: 0.7747 (tp40) cc_final: 0.7534 (tp40) REVERT: B 901 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8759 (mm) REVERT: C 154 PHE cc_start: 0.9384 (m-80) cc_final: 0.8762 (m-80) REVERT: C 268 TYR cc_start: 0.8696 (t80) cc_final: 0.8476 (t80) REVERT: C 298 MET cc_start: 0.8379 (mpp) cc_final: 0.8153 (mpp) REVERT: C 420 GLN cc_start: 0.7840 (mp10) cc_final: 0.7494 (tp40) REVERT: C 901 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8765 (mm) REVERT: D 154 PHE cc_start: 0.9384 (m-80) cc_final: 0.8763 (m-80) REVERT: D 268 TYR cc_start: 0.8691 (t80) cc_final: 0.8470 (t80) REVERT: D 298 MET cc_start: 0.8385 (mpp) cc_final: 0.8156 (mpp) REVERT: D 420 GLN cc_start: 0.7741 (tp40) cc_final: 0.7527 (tp40) REVERT: D 901 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8762 (mm) outliers start: 40 outliers final: 25 residues processed: 286 average time/residue: 1.0952 time to fit residues: 380.6582 Evaluate side-chains 266 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 237 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 941 ASP Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 895 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 941 ASP Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 325 optimal weight: 3.9990 chunk 344 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 308 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29256 Z= 0.226 Angle : 0.528 8.216 39644 Z= 0.260 Chirality : 0.041 0.136 4456 Planarity : 0.003 0.044 5020 Dihedral : 6.843 85.181 3972 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.77 % Allowed : 10.59 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3524 helix: 0.56 (0.13), residues: 1736 sheet: -2.26 (0.27), residues: 372 loop : -0.01 (0.18), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 235 HIS 0.003 0.001 HIS B 383 PHE 0.025 0.002 PHE B 300 TYR 0.012 0.001 TYR B1025 ARG 0.005 0.000 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 254 time to evaluate : 3.124 Fit side-chains REVERT: A 19 PHE cc_start: 0.8732 (m-80) cc_final: 0.8284 (m-80) REVERT: A 150 MET cc_start: 0.9025 (ppp) cc_final: 0.8699 (pp-130) REVERT: A 154 PHE cc_start: 0.9378 (m-80) cc_final: 0.8890 (m-80) REVERT: A 268 TYR cc_start: 0.8698 (t80) cc_final: 0.8462 (t80) REVERT: A 395 MET cc_start: 0.8262 (mpp) cc_final: 0.7734 (mpp) REVERT: A 488 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8693 (mm) REVERT: A 761 MET cc_start: 0.8347 (ttp) cc_final: 0.8109 (ttm) REVERT: A 901 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8782 (mm) REVERT: B 150 MET cc_start: 0.9027 (ppp) cc_final: 0.8701 (pp-130) REVERT: B 154 PHE cc_start: 0.9377 (m-80) cc_final: 0.8892 (m-80) REVERT: B 246 GLU cc_start: 0.8751 (tp30) cc_final: 0.8380 (tp30) REVERT: B 268 TYR cc_start: 0.8697 (t80) cc_final: 0.8463 (t80) REVERT: B 300 PHE cc_start: 0.8675 (t80) cc_final: 0.8385 (t80) REVERT: B 395 MET cc_start: 0.8236 (mpp) cc_final: 0.7702 (mpp) REVERT: B 488 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8693 (mm) REVERT: B 761 MET cc_start: 0.8340 (ttp) cc_final: 0.8101 (ttm) REVERT: B 901 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8780 (mm) REVERT: C 19 PHE cc_start: 0.8728 (m-80) cc_final: 0.8278 (m-80) REVERT: C 150 MET cc_start: 0.9026 (ppp) cc_final: 0.8701 (pp-130) REVERT: C 154 PHE cc_start: 0.9379 (m-80) cc_final: 0.8892 (m-80) REVERT: C 268 TYR cc_start: 0.8700 (t80) cc_final: 0.8464 (t80) REVERT: C 395 MET cc_start: 0.8236 (mpp) cc_final: 0.7723 (mpp) REVERT: C 420 GLN cc_start: 0.7857 (mp10) cc_final: 0.7506 (tp40) REVERT: C 488 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8684 (mm) REVERT: C 761 MET cc_start: 0.8342 (ttp) cc_final: 0.8105 (ttm) REVERT: C 901 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8781 (mm) REVERT: D 150 MET cc_start: 0.9026 (ppp) cc_final: 0.8700 (pp-130) REVERT: D 154 PHE cc_start: 0.9379 (m-80) cc_final: 0.8893 (m-80) REVERT: D 246 GLU cc_start: 0.8745 (tp30) cc_final: 0.8370 (tp30) REVERT: D 268 TYR cc_start: 0.8695 (t80) cc_final: 0.8462 (t80) REVERT: D 395 MET cc_start: 0.8256 (mpp) cc_final: 0.7747 (mpp) REVERT: D 488 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8694 (mm) REVERT: D 496 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7737 (mtm) REVERT: D 761 MET cc_start: 0.8345 (ttp) cc_final: 0.8107 (ttm) REVERT: D 901 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8783 (mm) outliers start: 55 outliers final: 19 residues processed: 293 average time/residue: 1.0317 time to fit residues: 373.6075 Evaluate side-chains 270 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 242 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 941 ASP Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 895 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 941 ASP Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 256 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 293 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 175 optimal weight: 0.8980 chunk 308 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 29256 Z= 0.207 Angle : 0.536 10.622 39644 Z= 0.263 Chirality : 0.041 0.135 4456 Planarity : 0.003 0.039 5020 Dihedral : 6.600 85.453 3972 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.61 % Allowed : 12.39 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3524 helix: 0.57 (0.13), residues: 1736 sheet: -2.24 (0.27), residues: 372 loop : 0.03 (0.18), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 235 HIS 0.003 0.001 HIS B 354 PHE 0.033 0.002 PHE B 296 TYR 0.010 0.001 TYR B1025 ARG 0.006 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 252 time to evaluate : 3.661 Fit side-chains REVERT: A 19 PHE cc_start: 0.8659 (m-80) cc_final: 0.8174 (m-80) REVERT: A 150 MET cc_start: 0.9151 (ppp) cc_final: 0.8844 (pp-130) REVERT: A 154 PHE cc_start: 0.9410 (m-80) cc_final: 0.8883 (m-80) REVERT: A 246 GLU cc_start: 0.8730 (tp30) cc_final: 0.8398 (tp30) REVERT: A 268 TYR cc_start: 0.8726 (t80) cc_final: 0.8503 (t80) REVERT: A 298 MET cc_start: 0.8566 (mpp) cc_final: 0.8358 (mpp) REVERT: A 395 MET cc_start: 0.8318 (mpp) cc_final: 0.7757 (mpp) REVERT: A 488 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8685 (mm) REVERT: A 496 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7754 (mtm) REVERT: A 524 MET cc_start: 0.7776 (ttm) cc_final: 0.7572 (ttm) REVERT: A 761 MET cc_start: 0.8299 (ttp) cc_final: 0.8042 (ttm) REVERT: A 901 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8795 (mm) REVERT: B 150 MET cc_start: 0.9152 (ppp) cc_final: 0.8847 (pp-130) REVERT: B 154 PHE cc_start: 0.9401 (m-80) cc_final: 0.8903 (m-80) REVERT: B 246 GLU cc_start: 0.8797 (tp30) cc_final: 0.8415 (tp30) REVERT: B 268 TYR cc_start: 0.8726 (t80) cc_final: 0.8502 (t80) REVERT: B 298 MET cc_start: 0.8566 (mpp) cc_final: 0.8355 (mpp) REVERT: B 300 PHE cc_start: 0.8728 (t80) cc_final: 0.8369 (t80) REVERT: B 395 MET cc_start: 0.8327 (mpp) cc_final: 0.7798 (mpp) REVERT: B 488 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8685 (mm) REVERT: B 496 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7756 (mtm) REVERT: B 761 MET cc_start: 0.8293 (ttp) cc_final: 0.8035 (ttm) REVERT: B 901 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8793 (mm) REVERT: C 19 PHE cc_start: 0.8657 (m-80) cc_final: 0.8168 (m-80) REVERT: C 150 MET cc_start: 0.9151 (ppp) cc_final: 0.8845 (pp-130) REVERT: C 154 PHE cc_start: 0.9411 (m-80) cc_final: 0.8884 (m-80) REVERT: C 246 GLU cc_start: 0.8751 (tp30) cc_final: 0.8535 (tp30) REVERT: C 268 TYR cc_start: 0.8729 (t80) cc_final: 0.8507 (t80) REVERT: C 298 MET cc_start: 0.8568 (mpp) cc_final: 0.8361 (mpp) REVERT: C 395 MET cc_start: 0.8328 (mpp) cc_final: 0.7800 (mpp) REVERT: C 420 GLN cc_start: 0.7821 (mp10) cc_final: 0.7532 (tp40) REVERT: C 488 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8678 (mm) REVERT: C 761 MET cc_start: 0.8293 (ttp) cc_final: 0.8035 (ttm) REVERT: C 901 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8797 (mm) REVERT: D 150 MET cc_start: 0.9151 (ppp) cc_final: 0.8845 (pp-130) REVERT: D 154 PHE cc_start: 0.9404 (m-80) cc_final: 0.8904 (m-80) REVERT: D 246 GLU cc_start: 0.8770 (tp30) cc_final: 0.8414 (tp30) REVERT: D 298 MET cc_start: 0.8565 (mpp) cc_final: 0.8359 (mpp) REVERT: D 488 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8687 (mm) REVERT: D 496 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7773 (mtm) REVERT: D 524 MET cc_start: 0.7770 (ttm) cc_final: 0.7568 (ttm) REVERT: D 761 MET cc_start: 0.8300 (ttp) cc_final: 0.8041 (ttm) REVERT: D 901 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8796 (mm) outliers start: 50 outliers final: 19 residues processed: 291 average time/residue: 1.0861 time to fit residues: 387.6114 Evaluate side-chains 269 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 941 ASP Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 895 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 941 ASP Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 6.9990 chunk 309 optimal weight: 0.6980 chunk 68 optimal weight: 0.0570 chunk 202 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 344 optimal weight: 0.8980 chunk 285 optimal weight: 30.0000 chunk 159 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 180 optimal weight: 50.0000 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29256 Z= 0.165 Angle : 0.531 14.428 39644 Z= 0.256 Chirality : 0.041 0.223 4456 Planarity : 0.003 0.039 5020 Dihedral : 6.367 86.123 3972 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.64 % Allowed : 13.42 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 3524 helix: 0.62 (0.13), residues: 1744 sheet: -2.13 (0.27), residues: 372 loop : 0.03 (0.18), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 789 HIS 0.003 0.001 HIS A 354 PHE 0.029 0.001 PHE A 241 TYR 0.009 0.001 TYR B 268 ARG 0.008 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 257 time to evaluate : 3.254 Fit side-chains REVERT: A 19 PHE cc_start: 0.8652 (m-80) cc_final: 0.8165 (m-80) REVERT: A 150 MET cc_start: 0.9156 (ppp) cc_final: 0.8829 (pp-130) REVERT: A 154 PHE cc_start: 0.9428 (m-80) cc_final: 0.8903 (m-80) REVERT: A 246 GLU cc_start: 0.8787 (tp30) cc_final: 0.8565 (tp30) REVERT: A 395 MET cc_start: 0.8337 (mpp) cc_final: 0.7755 (mpp) REVERT: A 488 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8650 (mm) REVERT: A 496 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7751 (mtm) REVERT: A 761 MET cc_start: 0.8150 (ttp) cc_final: 0.7861 (mtm) REVERT: A 901 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8823 (mm) REVERT: B 150 MET cc_start: 0.9159 (ppp) cc_final: 0.8832 (pp-130) REVERT: B 154 PHE cc_start: 0.9427 (m-80) cc_final: 0.8904 (m-80) REVERT: B 246 GLU cc_start: 0.8762 (tp30) cc_final: 0.8400 (tp30) REVERT: B 395 MET cc_start: 0.8348 (mpp) cc_final: 0.7775 (mpp) REVERT: B 488 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8672 (mm) REVERT: B 496 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7756 (mtm) REVERT: B 761 MET cc_start: 0.8141 (ttp) cc_final: 0.7853 (mtm) REVERT: B 901 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8819 (mm) REVERT: C 19 PHE cc_start: 0.8652 (m-80) cc_final: 0.8160 (m-80) REVERT: C 150 MET cc_start: 0.9157 (ppp) cc_final: 0.8832 (pp-130) REVERT: C 154 PHE cc_start: 0.9428 (m-80) cc_final: 0.8904 (m-80) REVERT: C 246 GLU cc_start: 0.8819 (tp30) cc_final: 0.8536 (tp30) REVERT: C 395 MET cc_start: 0.8348 (mpp) cc_final: 0.7777 (mpp) REVERT: C 488 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8669 (mm) REVERT: C 496 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7773 (mtm) REVERT: C 761 MET cc_start: 0.8133 (ttp) cc_final: 0.7844 (mtm) REVERT: C 901 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8823 (mm) REVERT: D 150 MET cc_start: 0.9157 (ppp) cc_final: 0.8830 (pp-130) REVERT: D 154 PHE cc_start: 0.9429 (m-80) cc_final: 0.8904 (m-80) REVERT: D 246 GLU cc_start: 0.8759 (tp30) cc_final: 0.8402 (tp30) REVERT: D 488 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8652 (mm) REVERT: D 496 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7742 (mtm) REVERT: D 761 MET cc_start: 0.8145 (ttp) cc_final: 0.7859 (mtm) REVERT: D 901 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8823 (mm) outliers start: 51 outliers final: 23 residues processed: 297 average time/residue: 1.0532 time to fit residues: 383.0677 Evaluate side-chains 274 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 239 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 941 ASP Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 895 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 941 ASP Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 0.0770 chunk 38 optimal weight: 0.7980 chunk 196 optimal weight: 0.2980 chunk 251 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 289 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 343 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 209 optimal weight: 0.0570 chunk 158 optimal weight: 0.9980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 29256 Z= 0.153 Angle : 0.548 13.913 39644 Z= 0.263 Chirality : 0.040 0.226 4456 Planarity : 0.003 0.039 5020 Dihedral : 6.221 86.316 3972 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.38 % Allowed : 14.80 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3524 helix: 0.68 (0.13), residues: 1728 sheet: -2.02 (0.27), residues: 372 loop : -0.04 (0.18), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 789 HIS 0.002 0.000 HIS C 383 PHE 0.034 0.001 PHE A 296 TYR 0.017 0.001 TYR B 268 ARG 0.008 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 262 time to evaluate : 3.418 Fit side-chains REVERT: A 19 PHE cc_start: 0.8661 (m-80) cc_final: 0.8197 (m-80) REVERT: A 395 MET cc_start: 0.8336 (mpp) cc_final: 0.7751 (mpp) REVERT: A 488 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8645 (mm) REVERT: A 496 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7739 (mtm) REVERT: A 761 MET cc_start: 0.8123 (ttp) cc_final: 0.7831 (mtm) REVERT: A 901 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8793 (mm) REVERT: B 246 GLU cc_start: 0.8737 (tp30) cc_final: 0.8407 (tp30) REVERT: B 395 MET cc_start: 0.8345 (mpp) cc_final: 0.7770 (mpp) REVERT: B 488 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8645 (mm) REVERT: B 496 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7741 (mtm) REVERT: B 761 MET cc_start: 0.8117 (ttp) cc_final: 0.7826 (mtm) REVERT: B 901 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8789 (mm) REVERT: C 19 PHE cc_start: 0.8664 (m-80) cc_final: 0.8197 (m-80) REVERT: C 246 GLU cc_start: 0.8784 (tp30) cc_final: 0.8543 (tp30) REVERT: C 395 MET cc_start: 0.8345 (mpp) cc_final: 0.7769 (mpp) REVERT: C 488 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8661 (mm) REVERT: C 496 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7736 (mtm) REVERT: C 761 MET cc_start: 0.8121 (ttp) cc_final: 0.7827 (mtm) REVERT: C 901 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8789 (mm) REVERT: D 150 MET cc_start: 0.9158 (ppp) cc_final: 0.8839 (ppp) REVERT: D 154 PHE cc_start: 0.9426 (m-80) cc_final: 0.8827 (m-80) REVERT: D 246 GLU cc_start: 0.8738 (tp30) cc_final: 0.8408 (tp30) REVERT: D 488 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8654 (mm) REVERT: D 496 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7667 (mtm) REVERT: D 761 MET cc_start: 0.8126 (ttp) cc_final: 0.7834 (mtm) REVERT: D 901 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8794 (mm) outliers start: 43 outliers final: 23 residues processed: 296 average time/residue: 1.1244 time to fit residues: 404.4219 Evaluate side-chains 280 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 245 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 941 ASP Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 895 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 941 ASP Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 204 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 218 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 269 optimal weight: 50.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 29256 Z= 0.297 Angle : 0.620 17.808 39644 Z= 0.297 Chirality : 0.043 0.264 4456 Planarity : 0.003 0.037 5020 Dihedral : 6.211 85.907 3972 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.03 % Allowed : 14.90 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3524 helix: 0.56 (0.13), residues: 1736 sheet: -2.04 (0.28), residues: 348 loop : 0.01 (0.18), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 391 HIS 0.005 0.001 HIS A 260 PHE 0.037 0.002 PHE B 296 TYR 0.015 0.001 TYR C 268 ARG 0.008 0.000 ARG C 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 266 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8705 (m-80) cc_final: 0.8223 (m-80) REVERT: A 488 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8780 (mm) REVERT: A 496 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7865 (mtm) REVERT: A 761 MET cc_start: 0.8172 (ttp) cc_final: 0.7884 (mtm) REVERT: B 19 PHE cc_start: 0.8702 (m-80) cc_final: 0.8216 (m-80) REVERT: B 154 PHE cc_start: 0.9420 (m-80) cc_final: 0.8783 (m-80) REVERT: B 488 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8769 (mm) REVERT: B 496 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7869 (mtm) REVERT: B 761 MET cc_start: 0.8167 (ttp) cc_final: 0.7874 (mtm) REVERT: C 19 PHE cc_start: 0.8701 (m-80) cc_final: 0.8214 (m-80) REVERT: C 246 GLU cc_start: 0.8712 (tp30) cc_final: 0.8496 (tp30) REVERT: C 488 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8780 (mm) REVERT: C 496 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7879 (mtm) REVERT: C 761 MET cc_start: 0.8170 (ttp) cc_final: 0.7882 (mtm) REVERT: D 19 PHE cc_start: 0.8707 (m-80) cc_final: 0.8223 (m-80) REVERT: D 150 MET cc_start: 0.9166 (ppp) cc_final: 0.8839 (ppp) REVERT: D 154 PHE cc_start: 0.9427 (m-80) cc_final: 0.8824 (m-80) REVERT: D 488 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8717 (mm) REVERT: D 496 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7827 (mtm) REVERT: D 761 MET cc_start: 0.8176 (ttp) cc_final: 0.7885 (mtm) outliers start: 63 outliers final: 36 residues processed: 314 average time/residue: 1.0820 time to fit residues: 413.8996 Evaluate side-chains 286 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 242 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 941 ASP Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 895 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 936 THR Chi-restraints excluded: chain D residue 941 ASP Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 3.9990 chunk 328 optimal weight: 0.7980 chunk 299 optimal weight: 4.9990 chunk 319 optimal weight: 0.6980 chunk 192 optimal weight: 6.9990 chunk 139 optimal weight: 0.0770 chunk 251 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 288 optimal weight: 4.9990 chunk 302 optimal weight: 0.0870 chunk 318 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 29256 Z= 0.181 Angle : 0.629 17.355 39644 Z= 0.298 Chirality : 0.041 0.323 4456 Planarity : 0.003 0.040 5020 Dihedral : 6.131 86.072 3972 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.29 % Allowed : 16.38 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3524 helix: 0.51 (0.13), residues: 1760 sheet: -2.08 (0.27), residues: 372 loop : 0.07 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 264 HIS 0.002 0.001 HIS B 383 PHE 0.037 0.001 PHE A 296 TYR 0.015 0.001 TYR B 268 ARG 0.009 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 242 time to evaluate : 3.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8686 (m-80) cc_final: 0.8031 (m-80) REVERT: A 488 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8673 (mm) REVERT: A 496 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7749 (mtm) REVERT: A 761 MET cc_start: 0.8138 (ttp) cc_final: 0.7845 (mtm) REVERT: A 901 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8823 (mm) REVERT: B 19 PHE cc_start: 0.8691 (m-80) cc_final: 0.8031 (m-80) REVERT: B 488 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8652 (mm) REVERT: B 496 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7726 (mtm) REVERT: B 761 MET cc_start: 0.8129 (ttp) cc_final: 0.7836 (mtm) REVERT: B 901 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8823 (mm) REVERT: C 19 PHE cc_start: 0.8685 (m-80) cc_final: 0.8026 (m-80) REVERT: C 246 GLU cc_start: 0.8721 (tp30) cc_final: 0.8473 (tp30) REVERT: C 488 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8674 (mm) REVERT: C 496 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7741 (mtm) REVERT: C 761 MET cc_start: 0.8134 (ttp) cc_final: 0.7842 (mtm) REVERT: C 901 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8824 (mm) REVERT: D 19 PHE cc_start: 0.8695 (m-80) cc_final: 0.8036 (m-80) REVERT: D 150 MET cc_start: 0.9099 (ppp) cc_final: 0.8802 (ppp) REVERT: D 154 PHE cc_start: 0.9429 (m-80) cc_final: 0.8819 (m-80) REVERT: D 488 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8645 (mm) REVERT: D 496 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7695 (mtm) REVERT: D 761 MET cc_start: 0.8137 (ttp) cc_final: 0.7844 (mtm) REVERT: D 901 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8819 (mm) outliers start: 40 outliers final: 23 residues processed: 273 average time/residue: 0.9760 time to fit residues: 332.8386 Evaluate side-chains 271 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 236 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 941 ASP Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 895 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 941 ASP Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 0.9990 chunk 338 optimal weight: 0.7980 chunk 206 optimal weight: 0.8980 chunk 160 optimal weight: 0.2980 chunk 235 optimal weight: 0.0060 chunk 354 optimal weight: 0.6980 chunk 326 optimal weight: 3.9990 chunk 282 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 29256 Z= 0.177 Angle : 0.638 16.818 39644 Z= 0.301 Chirality : 0.041 0.349 4456 Planarity : 0.003 0.041 5020 Dihedral : 6.024 86.210 3972 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.19 % Allowed : 16.76 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3524 helix: 0.62 (0.13), residues: 1724 sheet: -2.00 (0.27), residues: 372 loop : 0.07 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 789 HIS 0.002 0.000 HIS C 383 PHE 0.043 0.002 PHE B 296 TYR 0.015 0.001 TYR B 268 ARG 0.009 0.000 ARG B 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7048 Ramachandran restraints generated. 3524 Oldfield, 0 Emsley, 3524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 247 time to evaluate : 3.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8762 (m-80) cc_final: 0.8080 (m-80) REVERT: A 488 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8664 (mm) REVERT: A 496 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7727 (mtm) REVERT: A 761 MET cc_start: 0.8129 (ttp) cc_final: 0.7844 (mtm) REVERT: A 901 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8808 (mm) REVERT: B 19 PHE cc_start: 0.8772 (m-80) cc_final: 0.8085 (m-80) REVERT: B 488 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8667 (mm) REVERT: B 496 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7701 (mtm) REVERT: B 761 MET cc_start: 0.8122 (ttp) cc_final: 0.7835 (mtm) REVERT: B 901 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8811 (mm) REVERT: C 19 PHE cc_start: 0.8759 (m-80) cc_final: 0.8074 (m-80) REVERT: C 488 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8662 (mm) REVERT: C 496 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7768 (mtm) REVERT: C 761 MET cc_start: 0.8127 (ttp) cc_final: 0.7838 (mtm) REVERT: C 901 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8813 (mm) REVERT: D 19 PHE cc_start: 0.8771 (m-80) cc_final: 0.8085 (m-80) REVERT: D 488 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8649 (mm) REVERT: D 496 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7694 (mtm) REVERT: D 761 MET cc_start: 0.8128 (ttp) cc_final: 0.7841 (mtm) REVERT: D 901 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8806 (mm) outliers start: 37 outliers final: 24 residues processed: 276 average time/residue: 1.0398 time to fit residues: 365.6795 Evaluate side-chains 272 residues out of total 3108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 236 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 901 LEU Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 941 ASP Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 895 ASP Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 941 ASP Chi-restraints excluded: chain D residue 969 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 0.5980 chunk 300 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 260 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 290 optimal weight: 0.3980 chunk 35 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.156287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.097774 restraints weight = 40753.637| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.85 r_work: 0.3275 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 29256 Z= 0.208 Angle : 0.645 18.240 39644 Z= 0.303 Chirality : 0.041 0.189 4456 Planarity : 0.003 0.041 5020 Dihedral : 5.989 86.308 3972 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.38 % Allowed : 16.63 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3524 helix: 0.56 (0.13), residues: 1736 sheet: -1.93 (0.26), residues: 376 loop : 0.17 (0.18), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 391 HIS 0.003 0.001 HIS A 383 PHE 0.040 0.002 PHE B 296 TYR 0.014 0.001 TYR B 268 ARG 0.008 0.000 ARG D 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7806.84 seconds wall clock time: 139 minutes 59.47 seconds (8399.47 seconds total)