Starting phenix.real_space_refine on Thu Feb 15 07:53:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kna_22937/02_2024/7kna_22937.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kna_22937/02_2024/7kna_22937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kna_22937/02_2024/7kna_22937.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kna_22937/02_2024/7kna_22937.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kna_22937/02_2024/7kna_22937.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kna_22937/02_2024/7kna_22937.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 7314 2.51 5 N 1990 2.21 5 O 2241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 31": "OE1" <-> "OE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11593 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3755 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 3751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3751 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 3751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3751 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.31, per 1000 atoms: 0.54 Number of scatterers: 11593 At special positions: 0 Unit cell: (92.4, 85.05, 144.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2241 8.00 N 1990 7.00 C 7314 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 145 " distance=2.02 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 311 " distance=2.02 Simple disulfide: pdb=" SG CYS A 637 " - pdb=" SG CYS A 641 " distance=2.06 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 630 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 283 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 77 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 145 " distance=2.02 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 311 " distance=2.02 Simple disulfide: pdb=" SG CYS B 637 " - pdb=" SG CYS B 641 " distance=2.06 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 630 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 145 " distance=2.02 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 311 " distance=2.02 Simple disulfide: pdb=" SG CYS C 637 " - pdb=" SG CYS C 641 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 901 " - " ASN A 21 " " NAG A 902 " - " ASN A 33 " " NAG A 903 " - " ASN A 295 " " NAG A 904 " - " ASN A 647 " " NAG B 901 " - " ASN B 21 " " NAG B 902 " - " ASN B 33 " " NAG B 903 " - " ASN B 295 " " NAG B 904 " - " ASN B 647 " " NAG C 901 " - " ASN C 21 " " NAG C 902 " - " ASN C 33 " " NAG C 903 " - " ASN C 295 " " NAG C 904 " - " ASN C 647 " " NAG D 1 " - " ASN A 97 " " NAG E 1 " - " ASN A 284 " " NAG F 1 " - " ASN B 97 " " NAG G 1 " - " ASN B 284 " " NAG H 1 " - " ASN C 97 " " NAG I 1 " - " ASN C 284 " Time building additional restraints: 4.55 Conformation dependent library (CDL) restraints added in 2.2 seconds 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2694 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 33 sheets defined 26.7% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.772A pdb=" N GLU A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 530 through 551 Processing helix chain 'A' and resid 567 through 620 removed outlier: 3.649A pdb=" N GLU A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 618 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 647 removed outlier: 3.523A pdb=" N SER A 644 " --> pdb=" O THR A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 74 through 78 removed outlier: 3.772A pdb=" N GLU B 78 " --> pdb=" O PRO B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 193 through 202 Processing helix chain 'B' and resid 530 through 551 Processing helix chain 'B' and resid 567 through 620 removed outlier: 3.649A pdb=" N GLU B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG B 599 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 618 " --> pdb=" O LYS B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 647 removed outlier: 3.522A pdb=" N SER B 644 " --> pdb=" O THR B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 654 No H-bonds generated for 'chain 'B' and resid 652 through 654' Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.772A pdb=" N GLU C 78 " --> pdb=" O PRO C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 193 through 202 Processing helix chain 'C' and resid 530 through 551 Processing helix chain 'C' and resid 567 through 620 removed outlier: 3.648A pdb=" N GLU C 598 " --> pdb=" O LEU C 594 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG C 599 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN C 618 " --> pdb=" O LYS C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 647 removed outlier: 3.522A pdb=" N SER C 644 " --> pdb=" O THR C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 654 No H-bonds generated for 'chain 'C' and resid 652 through 654' Processing helix chain 'C' and resid 655 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 525 through 529 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.919A pdb=" N LEU A 51 " --> pdb=" O HIS A 281 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N CYS A 283 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 60 through 62 removed outlier: 6.388A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 89 " --> pdb=" O ILE A 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 118 through 124 removed outlier: 3.761A pdb=" N SER A 120 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU A 185 " --> pdb=" O PRO A 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 118 through 124 removed outlier: 3.761A pdb=" N SER A 120 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 142 through 147 removed outlier: 4.737A pdb=" N CYS A 145 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 170 through 175 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AB3, first strand: chain 'B' and resid 525 through 529 Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 54 removed outlier: 5.919A pdb=" N LEU B 51 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N CYS B 283 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.387A pdb=" N LEU B 60 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE B 89 " --> pdb=" O ILE B 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 118 through 124 removed outlier: 3.760A pdb=" N SER B 120 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU B 185 " --> pdb=" O PRO B 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 118 through 124 removed outlier: 3.760A pdb=" N SER B 120 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 142 through 147 removed outlier: 4.737A pdb=" N CYS B 145 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 170 through 175 Processing sheet with id=AC4, first strand: chain 'B' and resid 287 through 288 Processing sheet with id=AC5, first strand: chain 'C' and resid 525 through 529 Processing sheet with id=AC6, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.920A pdb=" N LEU C 51 " --> pdb=" O HIS C 281 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N CYS C 283 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 60 through 62 removed outlier: 6.387A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 89 " --> pdb=" O ILE C 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 118 through 124 removed outlier: 3.761A pdb=" N SER C 120 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU C 185 " --> pdb=" O PRO C 260 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 118 through 124 removed outlier: 3.761A pdb=" N SER C 120 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 142 through 147 removed outlier: 4.737A pdb=" N CYS C 145 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 170 through 175 Processing sheet with id=AD6, first strand: chain 'C' and resid 287 through 288 495 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 4.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2030 1.31 - 1.45: 3500 1.45 - 1.58: 6255 1.58 - 1.72: 15 1.72 - 1.86: 60 Bond restraints: 11860 Sorted by residual: bond pdb=" NE ARG A 663 " pdb=" CZ ARG A 663 " ideal model delta sigma weight residual 1.326 1.381 -0.055 1.10e-02 8.26e+03 2.54e+01 bond pdb=" NE ARG C 663 " pdb=" CZ ARG C 663 " ideal model delta sigma weight residual 1.326 1.381 -0.055 1.10e-02 8.26e+03 2.51e+01 bond pdb=" NE ARG B 663 " pdb=" CZ ARG B 663 " ideal model delta sigma weight residual 1.326 1.381 -0.055 1.10e-02 8.26e+03 2.51e+01 bond pdb=" C CYS A 100 " pdb=" O CYS A 100 " ideal model delta sigma weight residual 1.236 1.173 0.063 1.28e-02 6.10e+03 2.43e+01 bond pdb=" C CYS B 100 " pdb=" O CYS B 100 " ideal model delta sigma weight residual 1.236 1.173 0.063 1.28e-02 6.10e+03 2.40e+01 ... (remaining 11855 not shown) Histogram of bond angle deviations from ideal: 92.87 - 105.40: 248 105.40 - 117.92: 8971 117.92 - 130.44: 6808 130.44 - 142.96: 75 142.96 - 155.48: 3 Bond angle restraints: 16105 Sorted by residual: angle pdb=" C2 NAG C 902 " pdb=" N2 NAG C 902 " pdb=" C7 NAG C 902 " ideal model delta sigma weight residual 124.56 155.48 -30.92 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C2 NAG B 902 " pdb=" N2 NAG B 902 " pdb=" C7 NAG B 902 " ideal model delta sigma weight residual 124.56 155.47 -30.91 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C2 NAG A 902 " pdb=" N2 NAG A 902 " pdb=" C7 NAG A 902 " ideal model delta sigma weight residual 124.56 155.45 -30.89 3.00e+00 1.11e-01 1.06e+02 angle pdb=" CD1 LEU A 170 " pdb=" CG LEU A 170 " pdb=" CD2 LEU A 170 " ideal model delta sigma weight residual 110.80 92.87 17.93 2.20e+00 2.07e-01 6.64e+01 angle pdb=" CD1 LEU B 170 " pdb=" CG LEU B 170 " pdb=" CD2 LEU B 170 " ideal model delta sigma weight residual 110.80 92.88 17.92 2.20e+00 2.07e-01 6.64e+01 ... (remaining 16100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 7000 16.36 - 32.72: 288 32.72 - 49.07: 48 49.07 - 65.43: 30 65.43 - 81.79: 9 Dihedral angle restraints: 7375 sinusoidal: 3169 harmonic: 4206 Sorted by residual: dihedral pdb=" CB CYS A 65 " pdb=" SG CYS A 65 " pdb=" SG CYS A 77 " pdb=" CB CYS A 77 " ideal model delta sinusoidal sigma weight residual -86.00 -125.72 39.72 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" CB CYS B 65 " pdb=" SG CYS B 65 " pdb=" SG CYS B 77 " pdb=" CB CYS B 77 " ideal model delta sinusoidal sigma weight residual -86.00 -125.70 39.70 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CB CYS C 65 " pdb=" SG CYS C 65 " pdb=" SG CYS C 77 " pdb=" CB CYS C 77 " ideal model delta sinusoidal sigma weight residual -86.00 -125.69 39.69 1 1.00e+01 1.00e-02 2.21e+01 ... (remaining 7372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1643 0.134 - 0.268: 137 0.268 - 0.403: 50 0.403 - 0.537: 3 0.537 - 0.671: 3 Chirality restraints: 1836 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.45e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.32e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.27e+01 ... (remaining 1833 not shown) Planarity restraints: 2061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 97 " -0.034 2.00e-02 2.50e+03 3.43e-02 1.47e+01 pdb=" CG ASN C 97 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 97 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C 97 " 0.051 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 97 " -0.034 2.00e-02 2.50e+03 3.43e-02 1.47e+01 pdb=" CG ASN A 97 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 97 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 97 " 0.051 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 97 " 0.034 2.00e-02 2.50e+03 3.42e-02 1.46e+01 pdb=" CG ASN B 97 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 97 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 97 " -0.051 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.041 2.00e-02 2.50e+03 ... (remaining 2058 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 5075 2.92 - 3.42: 10525 3.42 - 3.91: 20377 3.91 - 4.41: 22896 4.41 - 4.90: 37998 Nonbonded interactions: 96871 Sorted by model distance: nonbonded pdb=" OD2 ASP C 137 " pdb=" NZ LYS C 139A" model vdw 2.426 2.520 nonbonded pdb=" OD2 ASP B 137 " pdb=" NZ LYS B 139A" model vdw 2.426 2.520 nonbonded pdb=" OD2 ASP A 137 " pdb=" NZ LYS A 139A" model vdw 2.427 2.520 nonbonded pdb=" O ASN B 269 " pdb=" N GLY B 271 " model vdw 2.532 2.520 nonbonded pdb=" O ASN C 269 " pdb=" N GLY C 271 " model vdw 2.532 2.520 ... (remaining 96866 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 11 through 659 or (resid 660 through 662 and (name N or na \ me CA or name C or name O or name CB )) or resid 663 or resid 901 through 904)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.000 Extract box with map and model: 4.070 Check model and map are aligned: 0.170 Set scattering table: 0.130 Process input model: 33.950 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 : 0.016 0.100 11860 Z= 1.034 Angle : 1.472 30.918 16105 Z= 0.927 Chirality : 0.098 0.671 1836 Planarity : 0.006 0.031 2043 Dihedral : 10.095 81.791 4627 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.88 % Favored : 97.91 % Rotamer: Outliers : 0.50 % Allowed : 0.76 % Favored : 98.74 % 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: 0.26 (0.19), residues: 1437 helix: 0.11 (0.23), residues: 375 sheet: 1.10 (0.30), residues: 258 loop : -0.01 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP A 133 HIS 0.004 0.001 HIS C 635 PHE 0.023 0.004 PHE C 209 TYR 0.035 0.006 TYR B 587 ARG 0.005 0.001 ARG C 599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 1.441 Fit side-chains REVERT: C 104 ASP cc_start: 0.6936 (m-30) cc_final: 0.6733 (m-30) outliers start: 6 outliers final: 3 residues processed: 145 average time/residue: 0.2940 time to fit residues: 58.1998 Evaluate side-chains 56 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain C residue 33 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7851 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11860 Z= 0.218 Angle : 0.573 6.693 16105 Z= 0.306 Chirality : 0.047 0.306 1836 Planarity : 0.004 0.046 2043 Dihedral : 5.253 28.777 2067 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.25 % Favored : 98.54 % Rotamer: Outliers : 1.17 % Allowed : 3.94 % Favored : 94.88 % 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: 0.94 (0.21), residues: 1437 helix: 1.61 (0.26), residues: 357 sheet: 0.71 (0.31), residues: 258 loop : 0.25 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 514 HIS 0.003 0.001 HIS C 604 PHE 0.018 0.002 PHE B 631 TYR 0.025 0.002 TYR A 650 ARG 0.005 0.001 ARG C 599 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 1.414 Fit side-chains REVERT: A 266 MET cc_start: 0.8028 (pp-130) cc_final: 0.7342 (ptt) REVERT: B 266 MET cc_start: 0.7963 (pp-130) cc_final: 0.7260 (ptt) REVERT: C 104 ASP cc_start: 0.6988 (m-30) cc_final: 0.6710 (m-30) REVERT: C 266 MET cc_start: 0.8092 (pp-130) cc_final: 0.7516 (ptt) REVERT: C 595 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7472 (mp) outliers start: 14 outliers final: 2 residues processed: 81 average time/residue: 0.2310 time to fit residues: 28.0300 Evaluate side-chains 43 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 595 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 0.0770 chunk 105 optimal weight: 0.8980 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN B 555 GLN C 555 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11860 Z= 0.317 Angle : 0.561 6.234 16105 Z= 0.296 Chirality : 0.046 0.244 1836 Planarity : 0.004 0.071 2043 Dihedral : 4.708 27.187 2061 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.01 % Allowed : 6.12 % Favored : 92.87 % 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: 0.49 (0.21), residues: 1437 helix: 1.50 (0.26), residues: 375 sheet: 0.04 (0.29), residues: 300 loop : -0.06 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 585 HIS 0.004 0.001 HIS B 18 PHE 0.012 0.002 PHE A 127 TYR 0.025 0.002 TYR A 650 ARG 0.005 0.000 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 1.517 Fit side-chains REVERT: A 266 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7745 (ptt) REVERT: B 266 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7487 (ptt) REVERT: C 104 ASP cc_start: 0.7060 (m-30) cc_final: 0.6787 (m-30) REVERT: C 110 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7450 (mm-30) REVERT: C 266 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7712 (ptt) outliers start: 12 outliers final: 4 residues processed: 56 average time/residue: 0.1759 time to fit residues: 17.4050 Evaluate side-chains 46 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 266 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS C 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11860 Z= 0.213 Angle : 0.485 6.613 16105 Z= 0.254 Chirality : 0.044 0.281 1836 Planarity : 0.004 0.059 2043 Dihedral : 4.326 28.240 2061 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.09 % Allowed : 6.63 % Favored : 92.28 % 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: 0.59 (0.22), residues: 1437 helix: 1.74 (0.27), residues: 375 sheet: -0.05 (0.33), residues: 270 loop : -0.03 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 159 HIS 0.003 0.001 HIS B 18 PHE 0.012 0.001 PHE A 631 TYR 0.024 0.001 TYR A 650 ARG 0.003 0.000 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 1.360 Fit side-chains REVERT: A 266 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7503 (ptt) REVERT: A 531 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8005 (tp) REVERT: B 266 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7580 (ptt) REVERT: C 110 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7399 (mm-30) REVERT: C 266 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7701 (ptt) outliers start: 13 outliers final: 5 residues processed: 50 average time/residue: 0.1988 time to fit residues: 16.7249 Evaluate side-chains 48 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 595 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 11860 Z= 0.412 Angle : 0.572 5.975 16105 Z= 0.297 Chirality : 0.047 0.267 1836 Planarity : 0.004 0.039 2043 Dihedral : 5.073 34.384 2061 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.68 % Allowed : 6.88 % Favored : 91.44 % 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: 0.18 (0.21), residues: 1437 helix: 1.64 (0.27), residues: 375 sheet: -0.39 (0.30), residues: 300 loop : -0.38 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 159 HIS 0.007 0.001 HIS A 18 PHE 0.013 0.002 PHE C 105 TYR 0.023 0.002 TYR A 650 ARG 0.003 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 44 time to evaluate : 1.383 Fit side-chains REVERT: A 110 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7678 (mm-30) REVERT: A 266 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7626 (ptt) REVERT: B 266 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7734 (ptt) REVERT: C 110 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7527 (mm-30) REVERT: C 266 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7792 (ptt) outliers start: 20 outliers final: 9 residues processed: 56 average time/residue: 0.1830 time to fit residues: 17.7289 Evaluate side-chains 50 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 595 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11860 Z= 0.198 Angle : 0.472 6.620 16105 Z= 0.247 Chirality : 0.044 0.266 1836 Planarity : 0.003 0.045 2043 Dihedral : 4.771 32.394 2061 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.34 % Allowed : 7.47 % Favored : 91.19 % 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: 0.44 (0.22), residues: 1437 helix: 1.96 (0.27), residues: 375 sheet: -0.48 (0.32), residues: 270 loop : -0.18 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 585 HIS 0.004 0.001 HIS B 18 PHE 0.008 0.001 PHE A 121 TYR 0.020 0.001 TYR A 650 ARG 0.001 0.000 ARG C 599 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 1.441 Fit side-chains REVERT: A 110 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7538 (mm-30) REVERT: A 266 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7623 (ptt) REVERT: B 266 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7701 (ptt) REVERT: C 110 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7390 (mm-30) REVERT: C 266 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7745 (ptt) outliers start: 16 outliers final: 7 residues processed: 52 average time/residue: 0.1981 time to fit residues: 17.2660 Evaluate side-chains 51 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 596 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.0020 chunk 79 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11860 Z= 0.234 Angle : 0.469 5.995 16105 Z= 0.245 Chirality : 0.044 0.269 1836 Planarity : 0.003 0.037 2043 Dihedral : 4.708 33.285 2061 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.01 % Allowed : 7.97 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.22), residues: 1437 helix: 2.12 (0.27), residues: 378 sheet: -0.42 (0.30), residues: 300 loop : -0.28 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 585 HIS 0.004 0.001 HIS B 18 PHE 0.008 0.001 PHE A 121 TYR 0.021 0.001 TYR A 650 ARG 0.003 0.000 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 1.536 Fit side-chains REVERT: A 110 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7546 (mm-30) REVERT: A 266 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7614 (ptt) REVERT: B 266 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7718 (ptt) REVERT: C 110 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7425 (mm-30) REVERT: C 266 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7739 (ptt) outliers start: 12 outliers final: 7 residues processed: 47 average time/residue: 0.1843 time to fit residues: 15.4271 Evaluate side-chains 48 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 596 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8029 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 11860 Z= 0.431 Angle : 0.561 5.856 16105 Z= 0.290 Chirality : 0.047 0.273 1836 Planarity : 0.004 0.034 2043 Dihedral : 5.463 43.589 2061 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.17 % Allowed : 8.14 % Favored : 90.69 % 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 (0.21), residues: 1437 helix: 1.87 (0.27), residues: 378 sheet: -0.78 (0.31), residues: 243 loop : -0.51 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 159 HIS 0.007 0.001 HIS A 18 PHE 0.011 0.002 PHE C 105 TYR 0.020 0.002 TYR A 650 ARG 0.002 0.000 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 1.487 Fit side-chains REVERT: A 110 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7621 (mm-30) REVERT: A 266 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7678 (ptt) REVERT: B 266 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7793 (ptt) REVERT: C 110 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7550 (mm-30) REVERT: C 266 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7842 (ptt) outliers start: 14 outliers final: 8 residues processed: 49 average time/residue: 0.1860 time to fit residues: 16.2148 Evaluate side-chains 49 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 596 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 0.4980 chunk 84 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11860 Z= 0.177 Angle : 0.469 6.209 16105 Z= 0.246 Chirality : 0.043 0.266 1836 Planarity : 0.003 0.042 2043 Dihedral : 5.054 41.372 2061 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.92 % Allowed : 8.56 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1437 helix: 2.13 (0.27), residues: 378 sheet: -0.96 (0.35), residues: 213 loop : -0.29 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 240 HIS 0.005 0.001 HIS A 18 PHE 0.008 0.001 PHE A 121 TYR 0.019 0.001 TYR A 650 ARG 0.003 0.000 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 1.404 Fit side-chains REVERT: A 110 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 266 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7608 (ptt) REVERT: B 266 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7736 (ptt) REVERT: C 110 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7354 (mm-30) REVERT: C 266 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7783 (ptt) outliers start: 11 outliers final: 8 residues processed: 48 average time/residue: 0.1745 time to fit residues: 14.9250 Evaluate side-chains 52 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 596 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 114 optimal weight: 0.0010 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- 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: 0.7991 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11860 Z= 0.272 Angle : 0.491 5.781 16105 Z= 0.255 Chirality : 0.044 0.270 1836 Planarity : 0.004 0.035 2043 Dihedral : 5.125 43.580 2061 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.01 % Allowed : 8.39 % Favored : 90.60 % 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 (0.22), residues: 1437 helix: 2.12 (0.27), residues: 378 sheet: -0.76 (0.32), residues: 243 loop : -0.41 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 585 HIS 0.005 0.001 HIS A 18 PHE 0.008 0.001 PHE B 121 TYR 0.021 0.002 TYR C 650 ARG 0.003 0.000 ARG B 599 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 1.334 Fit side-chains REVERT: A 110 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7558 (mm-30) REVERT: A 266 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7628 (ptt) REVERT: B 266 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7724 (ptt) REVERT: C 110 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7419 (mm-30) REVERT: C 266 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7765 (ptt) outliers start: 12 outliers final: 8 residues processed: 47 average time/residue: 0.1716 time to fit residues: 14.4527 Evaluate side-chains 51 residues out of total 1275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 596 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 105 optimal weight: 0.2980 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 47 optimal weight: 0.0060 chunk 117 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.113883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.090726 restraints weight = 18980.516| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.56 r_work: 0.2986 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11860 Z= 0.159 Angle : 0.458 7.182 16105 Z= 0.240 Chirality : 0.043 0.269 1836 Planarity : 0.003 0.044 2043 Dihedral : 4.798 39.631 2061 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.01 % Allowed : 8.56 % Favored : 90.44 % 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: 0.45 (0.22), residues: 1437 helix: 2.22 (0.27), residues: 381 sheet: -0.94 (0.35), residues: 213 loop : -0.22 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 514 HIS 0.004 0.001 HIS A 18 PHE 0.008 0.001 PHE A 121 TYR 0.028 0.001 TYR C 650 ARG 0.003 0.000 ARG B 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1920.26 seconds wall clock time: 36 minutes 29.87 seconds (2189.87 seconds total)