Starting phenix.real_space_refine on Wed Feb 14 21:44:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2i_16391/02_2024/8c2i_16391_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2i_16391/02_2024/8c2i_16391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2i_16391/02_2024/8c2i_16391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2i_16391/02_2024/8c2i_16391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2i_16391/02_2024/8c2i_16391_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2i_16391/02_2024/8c2i_16391_updated.pdb" } resolution = 2.7 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 ------------------------------------------------------------------------------- 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 63 5.16 5 C 6886 2.51 5 N 1591 2.21 5 O 1818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 515": "OD1" <-> "OD2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A ARG 624": "NH1" <-> "NH2" Residue "A PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 515": "OD1" <-> "OD2" Residue "B PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 623": "OE1" <-> "OE2" Residue "C ASP 515": "OD1" <-> "OD2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 590": "NH1" <-> "NH2" Residue "C PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 623": "OE1" <-> "OE2" Residue "C ARG 624": "NH1" <-> "NH2" Residue "C PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 515": "OD1" <-> "OD2" Residue "D PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 623": "OE1" <-> "OE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "H TYR 200": "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: 10366 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1092 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 139, 1063 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 139, 1063 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 1059 Chain: "B" Number of atoms: 1102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 137, 1055 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 137, 1055 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 1033 Chain: "C" Number of atoms: 1118 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 142, 1089 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 137} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 142, 1089 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 137} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 1085 Chain: "D" Number of atoms: 1102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 137, 1055 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 137, 1055 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 1033 Chain: "E" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "F" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "G" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 32 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 20 residue: pdb=" N AGLY A 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 584 " occ=0.50 residue: pdb=" N ACYS A 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 585 " occ=0.50 residue: pdb=" N AASP A 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A 586 " occ=0.50 residue: pdb=" N APHE A 619 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 619 " occ=0.50 residue: pdb=" N AGLN B 582 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 582 " occ=0.50 residue: pdb=" N AGLN B 583 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 583 " occ=0.50 residue: pdb=" N AGLY B 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 584 " occ=0.50 residue: pdb=" N ACYS B 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 585 " occ=0.50 residue: pdb=" N AASP B 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP B 586 " occ=0.50 residue: pdb=" N APHE B 619 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 619 " occ=0.50 residue: pdb=" N AGLY C 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY C 584 " occ=0.50 residue: pdb=" N ACYS C 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 585 " occ=0.50 ... (remaining 8 not shown) Time building chain proxies: 7.93, per 1000 atoms: 0.77 Number of scatterers: 10366 At special positions: 0 Unit cell: (97.52, 95.4, 87.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 8 15.00 O 1818 8.00 N 1591 7.00 C 6886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.01 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.06 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.04 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.02 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.06 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.04 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " 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: 4.49 Conformation dependent library (CDL) restraints added in 2.6 seconds 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2326 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 4 sheets defined 68.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 519 through 541 Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 592 through 621 Processing helix chain 'A' and resid 785 through 813 removed outlier: 3.777A pdb=" N ALA A 789 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLY A 790 " --> pdb=" O ASN A 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 519 through 541 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 592 through 625 Processing helix chain 'B' and resid 785 through 814 removed outlier: 3.529A pdb=" N ALA B 789 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY B 790 " --> pdb=" O ASN B 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 519 through 541 Processing helix chain 'C' and resid 569 through 580 Processing helix chain 'C' and resid 592 through 621 Processing helix chain 'C' and resid 785 through 813 removed outlier: 3.779A pdb=" N ALA C 789 " --> pdb=" O SER C 786 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLY C 790 " --> pdb=" O ASN C 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 514 No H-bonds generated for 'chain 'D' and resid 512 through 514' Processing helix chain 'D' and resid 519 through 541 Processing helix chain 'D' and resid 569 through 580 Processing helix chain 'D' and resid 592 through 621 Processing helix chain 'D' and resid 785 through 814 removed outlier: 3.511A pdb=" N ALA D 789 " --> pdb=" O SER D 786 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY D 790 " --> pdb=" O ASN D 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 93 through 103 Processing helix chain 'E' and resid 106 through 127 removed outlier: 4.249A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 161 Processing helix chain 'E' and resid 177 through 208 Processing helix chain 'F' and resid 6 through 29 Processing helix chain 'F' and resid 93 through 104 Processing helix chain 'F' and resid 106 through 126 removed outlier: 3.835A pdb=" N GLU F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 161 removed outlier: 4.066A pdb=" N ALA F 161 " --> pdb=" O SER F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 208 removed outlier: 3.683A pdb=" N ARG F 208 " --> pdb=" O HIS F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 29 Processing helix chain 'G' and resid 93 through 103 Processing helix chain 'G' and resid 106 through 127 removed outlier: 4.243A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 161 Processing helix chain 'G' and resid 177 through 208 Processing helix chain 'H' and resid 6 through 29 Processing helix chain 'H' and resid 93 through 104 Processing helix chain 'H' and resid 106 through 126 removed outlier: 3.839A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 161 removed outlier: 4.081A pdb=" N ALA H 161 " --> pdb=" O SER H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 208 removed outlier: 3.678A pdb=" N ARG H 208 " --> pdb=" O HIS H 204 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 59 through 61 Processing sheet with id= B, first strand: chain 'F' and resid 173 through 175 Processing sheet with id= C, first strand: chain 'G' and resid 59 through 61 Processing sheet with id= D, first strand: chain 'H' and resid 173 through 175 737 hydrogen bonds defined for protein. 1753 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: 2.96 Time building geometry restraints manager: 4.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1533 1.31 - 1.44: 3165 1.44 - 1.57: 5766 1.57 - 1.70: 16 1.70 - 1.83: 90 Bond restraints: 10570 Sorted by residual: bond pdb=" CA SER A 533 " pdb=" CB SER A 533 " ideal model delta sigma weight residual 1.528 1.473 0.055 1.56e-02 4.11e+03 1.24e+01 bond pdb=" C11 OLC B1002 " pdb=" C12 OLC B1002 " ideal model delta sigma weight residual 1.528 1.459 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C SER B 540 " pdb=" N ARG B 541 " ideal model delta sigma weight residual 1.333 1.282 0.051 1.50e-02 4.44e+03 1.16e+01 bond pdb=" CA SER C 593 " pdb=" CB SER C 593 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.59e-02 3.96e+03 1.00e+01 bond pdb=" CA SER A 593 " pdb=" CB SER A 593 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.58e-02 4.01e+03 9.94e+00 ... (remaining 10565 not shown) Histogram of bond angle deviations from ideal: 97.49 - 104.84: 97 104.84 - 112.19: 4884 112.19 - 119.53: 4049 119.53 - 126.88: 5065 126.88 - 134.23: 132 Bond angle restraints: 14227 Sorted by residual: angle pdb=" CA BPHE B 619 " pdb=" CB BPHE B 619 " pdb=" CG BPHE B 619 " ideal model delta sigma weight residual 113.80 119.38 -5.58 1.00e+00 1.00e+00 3.11e+01 angle pdb=" C PHE D 542 " pdb=" CA PHE D 542 " pdb=" CB PHE D 542 " ideal model delta sigma weight residual 110.42 120.50 -10.08 1.99e+00 2.53e-01 2.57e+01 angle pdb=" C BASP B 586 " pdb=" N ILE B 587 " pdb=" CA ILE B 587 " ideal model delta sigma weight residual 122.71 115.49 7.22 1.44e+00 4.82e-01 2.51e+01 angle pdb=" C BASP D 586 " pdb=" N ILE D 587 " pdb=" CA ILE D 587 " ideal model delta sigma weight residual 122.71 115.49 7.22 1.44e+00 4.82e-01 2.51e+01 angle pdb=" CG ARG E 74 " pdb=" CD ARG E 74 " pdb=" NE ARG E 74 " ideal model delta sigma weight residual 112.00 101.13 10.87 2.20e+00 2.07e-01 2.44e+01 ... (remaining 14222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.89: 5551 23.89 - 47.77: 413 47.77 - 71.66: 93 71.66 - 95.54: 22 95.54 - 119.43: 3 Dihedral angle restraints: 6082 sinusoidal: 2445 harmonic: 3637 Sorted by residual: dihedral pdb=" C ARG B 541 " pdb=" N ARG B 541 " pdb=" CA ARG B 541 " pdb=" CB ARG B 541 " ideal model delta harmonic sigma weight residual -122.60 -111.08 -11.52 0 2.50e+00 1.60e-01 2.12e+01 dihedral pdb=" CA ASN D 787 " pdb=" C ASN D 787 " pdb=" N VAL D 788 " pdb=" CA VAL D 788 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA VAL E 39 " pdb=" C VAL E 39 " pdb=" N CYS E 40 " pdb=" CA CYS E 40 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 6079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 963 0.063 - 0.126: 473 0.126 - 0.189: 122 0.189 - 0.252: 14 0.252 - 0.315: 5 Chirality restraints: 1577 Sorted by residual: chirality pdb=" CA PHE C 511 " pdb=" N PHE C 511 " pdb=" C PHE C 511 " pdb=" CB PHE C 511 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB VAL D 791 " pdb=" CA VAL D 791 " pdb=" CG1 VAL D 791 " pdb=" CG2 VAL D 791 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB VAL B 791 " pdb=" CA VAL B 791 " pdb=" CG1 VAL B 791 " pdb=" CG2 VAL B 791 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 1574 not shown) Planarity restraints: 1711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D1003 " 0.047 2.00e-02 2.50e+03 8.88e-02 7.89e+01 pdb=" C29 POV D1003 " -0.116 2.00e-02 2.50e+03 pdb="C210 POV D1003 " 0.117 2.00e-02 2.50e+03 pdb="C211 POV D1003 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC B1002 " 0.067 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C11 OLC B1002 " -0.026 2.00e-02 2.50e+03 pdb=" C8 OLC B1002 " 0.027 2.00e-02 2.50e+03 pdb=" C9 OLC B1002 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B1003 " -0.051 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C29 POV B1003 " 0.054 2.00e-02 2.50e+03 pdb="C210 POV B1003 " 0.047 2.00e-02 2.50e+03 pdb="C211 POV B1003 " -0.050 2.00e-02 2.50e+03 ... (remaining 1708 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1364 2.76 - 3.29: 10815 3.29 - 3.83: 17591 3.83 - 4.36: 20597 4.36 - 4.90: 35804 Nonbonded interactions: 86171 Sorted by model distance: nonbonded pdb=" O BGLN B 583 " pdb=" O BGLY B 584 " model vdw 2.222 3.040 nonbonded pdb=" O21 POV E1201 " pdb=" O31 POV E1201 " model vdw 2.330 2.432 nonbonded pdb=" N GLU G 55 " pdb=" OE1 GLU G 55 " model vdw 2.351 2.520 nonbonded pdb=" N GLU E 55 " pdb=" OE1 GLU E 55 " model vdw 2.354 2.520 nonbonded pdb=" N BASP B 586 " pdb=" OD1BASP B 586 " model vdw 2.354 2.520 ... (remaining 86166 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 506 through 546 or resid 567 through 581 or resid 587 thro \ ugh 618 or resid 620 through 624 or resid 780 through 815 or resid 1001 through \ 1002)) selection = (chain 'B' and (resid 506 through 545 or (resid 566 and (name N or name CA or na \ me C or name O or name CB )) or resid 567 through 581 or resid 587 through 618 o \ r resid 620 through 624 or resid 780 through 813 or (resid 814 through 815 and ( \ name N or name CA or name C or name O or name CB )) or resid 1001 through 1002)) \ selection = (chain 'C' and (resid 506 through 546 or resid 567 through 581 or resid 587 thro \ ugh 618 or resid 620 through 624 or resid 780 through 815 or resid 1001 through \ 1002)) selection = (chain 'D' and (resid 506 through 545 or (resid 566 and (name N or name CA or na \ me C or name O or name CB )) or resid 567 through 581 or resid 587 through 618 o \ r resid 620 through 624 or resid 780 through 813 or (resid 814 through 815 and ( \ name N or name CA or name C or name O or name CB )) or resid 1001 through 1002)) \ } ncs_group { reference = (chain 'E' and (resid 5 through 209 or (resid 1201 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) selection = (chain 'F' and (resid 5 through 209 or (resid 1301 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) selection = (chain 'G' and (resid 5 through 209 or (resid 1201 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) selection = (chain 'H' and (resid 5 through 209 or (resid 1301 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) } 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=0.50 max=1.00 mean=0.99 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.280 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 34.030 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 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:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.010 0.069 10570 Z= 0.649 Angle : 1.274 10.874 14227 Z= 0.820 Chirality : 0.075 0.315 1577 Planarity : 0.013 0.143 1711 Dihedral : 17.793 119.430 3732 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.09 % Rotamer: Outliers : 4.07 % Allowed : 3.30 % Favored : 92.63 % Cbeta Deviations : 0.26 % 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: 0.27 (0.22), residues: 1239 helix: 1.04 (0.16), residues: 934 sheet: -0.79 (1.05), residues: 20 loop : -2.66 (0.29), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.010 TRP D 602 HIS 0.017 0.004 HIS E 60 PHE 0.063 0.008 PHE D 567 TYR 0.041 0.009 TYR H 96 ARG 0.027 0.003 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 193 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.7287 (tt0) cc_final: 0.7014 (tp30) REVERT: A 588 SER cc_start: 0.9410 (OUTLIER) cc_final: 0.9064 (p) REVERT: A 590 ARG cc_start: 0.8927 (mtt180) cc_final: 0.8472 (mpp-170) REVERT: A 781 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8426 (p) REVERT: C 590 ARG cc_start: 0.8698 (mtt180) cc_final: 0.8168 (mtm-85) REVERT: C 623 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: D 566 GLU cc_start: 0.7343 (pt0) cc_final: 0.6638 (pm20) REVERT: D 590 ARG cc_start: 0.8852 (mpt-90) cc_final: 0.8229 (mtt90) REVERT: D 623 GLU cc_start: 0.8771 (tt0) cc_final: 0.8437 (mm-30) REVERT: E 37 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7791 (mtp85) REVERT: E 79 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7640 (mptp) REVERT: E 81 ASP cc_start: 0.7544 (m-30) cc_final: 0.7220 (t0) REVERT: E 160 ASN cc_start: 0.7976 (m-40) cc_final: 0.7644 (m110) REVERT: F 58 MET cc_start: 0.7849 (tpp) cc_final: 0.7645 (mmm) REVERT: F 65 ARG cc_start: 0.8099 (mpp-170) cc_final: 0.7441 (mtm-85) REVERT: F 78 LYS cc_start: 0.8089 (ptmm) cc_final: 0.7761 (pttt) REVERT: G 24 MET cc_start: 0.8743 (tpt) cc_final: 0.8382 (tpt) REVERT: G 79 LYS cc_start: 0.8364 (ttmm) cc_final: 0.7906 (mptt) REVERT: G 99 ARG cc_start: 0.8270 (tpp80) cc_final: 0.7982 (mmt-90) REVERT: G 184 PHE cc_start: 0.7804 (m-80) cc_final: 0.7537 (m-10) outliers start: 31 outliers final: 8 residues processed: 208 average time/residue: 1.2621 time to fit residues: 281.0899 Evaluate side-chains 168 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 157 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain G residue 174 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 0.0770 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 HIS E 204 HIS F 204 HIS G 198 HIS G 204 HIS H 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10570 Z= 0.154 Angle : 0.481 6.141 14227 Z= 0.273 Chirality : 0.037 0.178 1577 Planarity : 0.006 0.031 1711 Dihedral : 14.095 112.899 1745 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.69 % Allowed : 9.80 % Favored : 86.52 % 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: 2.07 (0.24), residues: 1239 helix: 2.19 (0.17), residues: 934 sheet: 0.04 (1.20), residues: 20 loop : -1.38 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 574 HIS 0.004 0.001 HIS E 198 PHE 0.020 0.001 PHE B 542 TYR 0.012 0.001 TYR C 519 ARG 0.007 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.7243 (tt0) cc_final: 0.6946 (tp30) REVERT: A 590 ARG cc_start: 0.8816 (mtt180) cc_final: 0.8358 (mpp-170) REVERT: C 590 ARG cc_start: 0.8684 (mtt180) cc_final: 0.8210 (mtm-85) REVERT: C 623 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8026 (mt-10) REVERT: D 566 GLU cc_start: 0.7298 (pt0) cc_final: 0.6714 (pm20) REVERT: D 590 ARG cc_start: 0.8734 (mpt-90) cc_final: 0.8143 (mtt90) REVERT: D 623 GLU cc_start: 0.8873 (tt0) cc_final: 0.8418 (mm-30) REVERT: E 37 ARG cc_start: 0.7982 (mtp-110) cc_final: 0.7638 (mtp85) REVERT: E 79 LYS cc_start: 0.7891 (mtmt) cc_final: 0.7645 (mptp) REVERT: E 81 ASP cc_start: 0.7672 (m-30) cc_final: 0.7262 (t0) REVERT: F 150 ILE cc_start: 0.7763 (tt) cc_final: 0.7511 (pt) REVERT: G 24 MET cc_start: 0.8642 (tpt) cc_final: 0.8340 (tpt) REVERT: G 58 MET cc_start: 0.7786 (tpt) cc_final: 0.7492 (tpp) REVERT: G 76 VAL cc_start: 0.7987 (t) cc_final: 0.7776 (p) REVERT: G 79 LYS cc_start: 0.8366 (ttmm) cc_final: 0.7877 (mptt) REVERT: G 184 PHE cc_start: 0.7703 (m-80) cc_final: 0.7448 (m-10) REVERT: G 205 GLN cc_start: 0.7301 (tt0) cc_final: 0.7074 (tt0) outliers start: 27 outliers final: 9 residues processed: 186 average time/residue: 1.3810 time to fit residues: 273.8739 Evaluate side-chains 171 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 31 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 109 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS G 160 ASN G 204 HIS H 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10570 Z= 0.147 Angle : 0.456 7.814 14227 Z= 0.255 Chirality : 0.036 0.164 1577 Planarity : 0.005 0.033 1711 Dihedral : 11.966 87.548 1731 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.59 % Allowed : 11.74 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.24), residues: 1239 helix: 2.36 (0.17), residues: 934 sheet: 0.10 (1.21), residues: 20 loop : -0.99 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 574 HIS 0.002 0.001 HIS E 60 PHE 0.019 0.001 PHE D 810 TYR 0.012 0.001 TYR A 519 ARG 0.009 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.7319 (tt0) cc_final: 0.7058 (tp30) REVERT: A 590 ARG cc_start: 0.8858 (mtt180) cc_final: 0.8425 (mpp-170) REVERT: A 623 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8668 (tt0) REVERT: B 809 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6567 (tt0) REVERT: C 590 ARG cc_start: 0.8827 (mtt180) cc_final: 0.8605 (mmt90) REVERT: C 623 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: C 625 MET cc_start: 0.6520 (mmm) cc_final: 0.6255 (mmt) REVERT: D 566 GLU cc_start: 0.7269 (pt0) cc_final: 0.6653 (pm20) REVERT: D 590 ARG cc_start: 0.8743 (mpt-90) cc_final: 0.8081 (mtt90) REVERT: D 623 GLU cc_start: 0.8818 (tt0) cc_final: 0.8428 (mm-30) REVERT: D 625 MET cc_start: 0.8934 (mtm) cc_final: 0.8710 (mtm) REVERT: E 10 MET cc_start: 0.8270 (tpp) cc_final: 0.7937 (tpt) REVERT: E 37 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7599 (mtt-85) REVERT: E 79 LYS cc_start: 0.7921 (mtmt) cc_final: 0.7638 (mptp) REVERT: E 81 ASP cc_start: 0.8000 (m-30) cc_final: 0.7553 (t0) REVERT: E 131 ARG cc_start: 0.5757 (tpt90) cc_final: 0.5557 (mmm-85) REVERT: F 36 SER cc_start: 0.8098 (t) cc_final: 0.7856 (p) REVERT: F 41 ARG cc_start: 0.4957 (ttt-90) cc_final: 0.4545 (ptp-170) REVERT: F 65 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.6666 (mtp85) REVERT: F 150 ILE cc_start: 0.7725 (tt) cc_final: 0.7520 (pt) REVERT: G 58 MET cc_start: 0.7648 (tpt) cc_final: 0.7403 (tpp) REVERT: G 65 ARG cc_start: 0.8106 (mtm-85) cc_final: 0.7521 (ptp90) REVERT: G 76 VAL cc_start: 0.7884 (t) cc_final: 0.7661 (p) REVERT: G 79 LYS cc_start: 0.8304 (ttmm) cc_final: 0.7865 (mptt) REVERT: G 184 PHE cc_start: 0.7715 (m-80) cc_final: 0.7471 (m-10) REVERT: G 205 GLN cc_start: 0.7237 (tt0) cc_final: 0.7019 (tt0) outliers start: 26 outliers final: 14 residues processed: 182 average time/residue: 1.4340 time to fit residues: 278.0482 Evaluate side-chains 177 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 162 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 HIS G 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10570 Z= 0.210 Angle : 0.475 7.587 14227 Z= 0.264 Chirality : 0.037 0.170 1577 Planarity : 0.005 0.031 1711 Dihedral : 12.105 89.423 1731 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.36 % Allowed : 12.22 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.24), residues: 1239 helix: 2.26 (0.17), residues: 934 sheet: -0.06 (1.26), residues: 20 loop : -0.86 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 574 HIS 0.010 0.001 HIS G 204 PHE 0.014 0.001 PHE D 810 TYR 0.016 0.001 TYR G 200 ARG 0.006 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.7407 (tt0) cc_final: 0.7188 (tp30) REVERT: A 590 ARG cc_start: 0.8803 (mtt180) cc_final: 0.8367 (mpp-170) REVERT: A 623 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8657 (tt0) REVERT: B 809 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6689 (mt-10) REVERT: C 590 ARG cc_start: 0.8896 (mtt180) cc_final: 0.8680 (mmt90) REVERT: C 623 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: D 590 ARG cc_start: 0.8756 (mpt-90) cc_final: 0.8062 (mtt90) REVERT: D 623 GLU cc_start: 0.8902 (tt0) cc_final: 0.8517 (mm-30) REVERT: E 10 MET cc_start: 0.8302 (tpp) cc_final: 0.7973 (tpt) REVERT: E 37 ARG cc_start: 0.8048 (mtp-110) cc_final: 0.7579 (mtt-85) REVERT: E 81 ASP cc_start: 0.7949 (m-30) cc_final: 0.7503 (t0) REVERT: E 131 ARG cc_start: 0.5787 (tpt90) cc_final: 0.5409 (mmm-85) REVERT: F 41 ARG cc_start: 0.4931 (ttt-90) cc_final: 0.4669 (ptp-170) REVERT: F 65 ARG cc_start: 0.7412 (mtm-85) cc_final: 0.6616 (mtp85) REVERT: F 150 ILE cc_start: 0.7756 (tt) cc_final: 0.7433 (pt) REVERT: G 58 MET cc_start: 0.7663 (tpt) cc_final: 0.7431 (tpp) REVERT: G 65 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.7695 (ptp90) REVERT: G 79 LYS cc_start: 0.8408 (ttmm) cc_final: 0.7909 (mptt) REVERT: G 184 PHE cc_start: 0.7791 (m-80) cc_final: 0.7550 (m-10) outliers start: 34 outliers final: 21 residues processed: 180 average time/residue: 1.3800 time to fit residues: 264.8044 Evaluate side-chains 180 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 0.0970 chunk 104 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 HIS G 160 ASN H 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10570 Z= 0.161 Angle : 0.432 6.629 14227 Z= 0.243 Chirality : 0.036 0.151 1577 Planarity : 0.005 0.030 1711 Dihedral : 11.217 88.906 1731 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.46 % Allowed : 12.90 % Favored : 82.64 % 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: 2.49 (0.24), residues: 1239 helix: 2.38 (0.17), residues: 934 sheet: 0.44 (1.29), residues: 20 loop : -0.79 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 574 HIS 0.002 0.001 HIS G 204 PHE 0.020 0.001 PHE D 542 TYR 0.014 0.001 TYR G 200 ARG 0.007 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.7372 (tt0) cc_final: 0.7150 (tp30) REVERT: A 590 ARG cc_start: 0.8809 (mtt180) cc_final: 0.8343 (mpp-170) REVERT: A 623 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8630 (tt0) REVERT: B 809 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6628 (mt-10) REVERT: C 590 ARG cc_start: 0.8893 (mtt180) cc_final: 0.8679 (mmt90) REVERT: C 623 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: D 590 ARG cc_start: 0.8761 (mpt-90) cc_final: 0.8064 (mtt90) REVERT: D 623 GLU cc_start: 0.8878 (tt0) cc_final: 0.8468 (mm-30) REVERT: E 10 MET cc_start: 0.8333 (tpp) cc_final: 0.8077 (tpt) REVERT: E 37 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7617 (mtt-85) REVERT: E 81 ASP cc_start: 0.7960 (m-30) cc_final: 0.7478 (t0) REVERT: E 131 ARG cc_start: 0.5753 (tpt90) cc_final: 0.5066 (mmm-85) REVERT: E 133 SER cc_start: 0.7406 (m) cc_final: 0.7195 (p) REVERT: F 41 ARG cc_start: 0.4819 (ttt-90) cc_final: 0.4531 (mtm180) REVERT: F 65 ARG cc_start: 0.7442 (mtm-85) cc_final: 0.6624 (mtp85) REVERT: F 150 ILE cc_start: 0.7780 (tt) cc_final: 0.7527 (pt) REVERT: G 58 MET cc_start: 0.7557 (tpt) cc_final: 0.7354 (tpp) REVERT: G 65 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7621 (ptp90) REVERT: G 79 LYS cc_start: 0.8414 (ttmm) cc_final: 0.7915 (mptt) REVERT: G 184 PHE cc_start: 0.7700 (m-80) cc_final: 0.7441 (m-10) outliers start: 35 outliers final: 22 residues processed: 179 average time/residue: 1.4662 time to fit residues: 279.0662 Evaluate side-chains 184 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 205 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 117 optimal weight: 0.4980 chunk 97 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 HIS G 160 ASN H 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10570 Z= 0.182 Angle : 0.448 7.454 14227 Z= 0.250 Chirality : 0.036 0.156 1577 Planarity : 0.005 0.030 1711 Dihedral : 10.978 89.402 1731 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.27 % Allowed : 13.29 % Favored : 82.44 % 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: 2.50 (0.24), residues: 1239 helix: 2.37 (0.17), residues: 934 sheet: 0.48 (1.28), residues: 20 loop : -0.75 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 574 HIS 0.004 0.001 HIS H 204 PHE 0.018 0.001 PHE D 542 TYR 0.013 0.001 TYR G 200 ARG 0.004 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7734 (mmm160) cc_final: 0.7420 (mmm-85) REVERT: A 566 GLU cc_start: 0.7387 (tt0) cc_final: 0.7157 (tp30) REVERT: A 590 ARG cc_start: 0.8779 (mtt180) cc_final: 0.8311 (mpp-170) REVERT: A 623 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8638 (tt0) REVERT: B 809 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6884 (mt-10) REVERT: C 590 ARG cc_start: 0.8898 (mtt180) cc_final: 0.8687 (mmt90) REVERT: C 623 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: D 590 ARG cc_start: 0.8813 (mpt-90) cc_final: 0.8074 (mtt90) REVERT: D 623 GLU cc_start: 0.8934 (tt0) cc_final: 0.8536 (mm-30) REVERT: E 10 MET cc_start: 0.8280 (tpp) cc_final: 0.8014 (tpt) REVERT: E 37 ARG cc_start: 0.8111 (mtp-110) cc_final: 0.7656 (mtt-85) REVERT: E 81 ASP cc_start: 0.7959 (m-30) cc_final: 0.7484 (t0) REVERT: E 131 ARG cc_start: 0.5637 (tpt90) cc_final: 0.5002 (mmm-85) REVERT: E 133 SER cc_start: 0.7294 (m) cc_final: 0.7085 (p) REVERT: F 41 ARG cc_start: 0.5258 (ttt-90) cc_final: 0.5021 (ptp-170) REVERT: F 65 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.6690 (mtp85) REVERT: F 150 ILE cc_start: 0.7771 (tt) cc_final: 0.7497 (pt) REVERT: G 65 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7624 (ptp90) REVERT: G 79 LYS cc_start: 0.8451 (ttmm) cc_final: 0.7912 (mptt) REVERT: G 184 PHE cc_start: 0.7828 (m-80) cc_final: 0.7596 (m-10) REVERT: H 203 LYS cc_start: 0.6984 (ttmm) cc_final: 0.6672 (ttmt) outliers start: 33 outliers final: 23 residues processed: 177 average time/residue: 1.4325 time to fit residues: 269.5441 Evaluate side-chains 185 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 205 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 5.9990 chunk 66 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 HIS G 160 ASN H 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10570 Z= 0.194 Angle : 0.457 7.235 14227 Z= 0.254 Chirality : 0.037 0.163 1577 Planarity : 0.005 0.031 1711 Dihedral : 11.128 89.468 1731 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.27 % Allowed : 14.06 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.24), residues: 1239 helix: 2.37 (0.17), residues: 934 sheet: 0.78 (1.34), residues: 20 loop : -0.72 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 574 HIS 0.004 0.001 HIS H 204 PHE 0.017 0.001 PHE D 542 TYR 0.014 0.001 TYR G 200 ARG 0.005 0.000 ARG E 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 165 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7737 (mmm160) cc_final: 0.7479 (mmm-85) REVERT: A 590 ARG cc_start: 0.8770 (mtt180) cc_final: 0.8307 (mpp-170) REVERT: A 623 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8643 (tt0) REVERT: B 809 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6856 (mt-10) REVERT: C 542 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7432 (p90) REVERT: C 590 ARG cc_start: 0.8894 (mtt180) cc_final: 0.8676 (mmt90) REVERT: C 623 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: D 590 ARG cc_start: 0.8812 (mpt-90) cc_final: 0.8065 (mtt90) REVERT: D 623 GLU cc_start: 0.8937 (tt0) cc_final: 0.8544 (mm-30) REVERT: E 10 MET cc_start: 0.8307 (tpp) cc_final: 0.8073 (tpt) REVERT: E 37 ARG cc_start: 0.8131 (mtp-110) cc_final: 0.7720 (mtt-85) REVERT: E 56 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7533 (mm-30) REVERT: E 81 ASP cc_start: 0.8102 (m-30) cc_final: 0.7607 (t0) REVERT: E 131 ARG cc_start: 0.5649 (tpt90) cc_final: 0.4986 (mmm-85) REVERT: F 41 ARG cc_start: 0.5347 (ttt-90) cc_final: 0.5097 (ptp-170) REVERT: F 65 ARG cc_start: 0.7414 (mtm-85) cc_final: 0.6695 (mtp85) REVERT: F 150 ILE cc_start: 0.7776 (tt) cc_final: 0.7491 (pt) REVERT: G 65 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7588 (ptp90) REVERT: G 79 LYS cc_start: 0.8449 (ttmm) cc_final: 0.7930 (mptt) REVERT: G 184 PHE cc_start: 0.7820 (m-80) cc_final: 0.7593 (m-10) outliers start: 33 outliers final: 23 residues processed: 183 average time/residue: 1.4504 time to fit residues: 282.4054 Evaluate side-chains 186 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 HIS G 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10570 Z= 0.240 Angle : 0.485 6.519 14227 Z= 0.270 Chirality : 0.038 0.168 1577 Planarity : 0.005 0.033 1711 Dihedral : 11.659 89.868 1731 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.36 % Allowed : 14.26 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.24), residues: 1239 helix: 2.30 (0.17), residues: 934 sheet: 0.92 (1.35), residues: 20 loop : -0.73 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 574 HIS 0.004 0.001 HIS H 204 PHE 0.022 0.001 PHE D 542 TYR 0.015 0.001 TYR G 200 ARG 0.004 0.000 ARG H 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 164 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7750 (mmm160) cc_final: 0.7496 (mmm-85) REVERT: A 590 ARG cc_start: 0.8741 (mtt180) cc_final: 0.8287 (mpp-170) REVERT: A 623 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8625 (tt0) REVERT: B 809 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6877 (mt-10) REVERT: C 542 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7445 (p90) REVERT: C 590 ARG cc_start: 0.8863 (mtt180) cc_final: 0.8648 (mmt90) REVERT: C 623 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: D 590 ARG cc_start: 0.8820 (mpt-90) cc_final: 0.8062 (mtt90) REVERT: D 623 GLU cc_start: 0.8919 (tt0) cc_final: 0.8537 (mm-30) REVERT: E 10 MET cc_start: 0.8307 (tpp) cc_final: 0.8071 (tpt) REVERT: E 37 ARG cc_start: 0.8155 (mtp-110) cc_final: 0.7720 (mtt-85) REVERT: E 56 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7490 (mm-30) REVERT: E 81 ASP cc_start: 0.8101 (m-30) cc_final: 0.7612 (t0) REVERT: E 131 ARG cc_start: 0.5297 (tpt90) cc_final: 0.4942 (mmm-85) REVERT: F 41 ARG cc_start: 0.5643 (ttt-90) cc_final: 0.5394 (ptp-170) REVERT: F 65 ARG cc_start: 0.7474 (mtm-85) cc_final: 0.6709 (mtp85) REVERT: F 150 ILE cc_start: 0.7765 (tt) cc_final: 0.7409 (pt) REVERT: G 65 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7605 (ptp90) REVERT: G 79 LYS cc_start: 0.8424 (ttmm) cc_final: 0.7936 (mptt) outliers start: 34 outliers final: 22 residues processed: 181 average time/residue: 1.4244 time to fit residues: 274.7689 Evaluate side-chains 185 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 150 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 HIS G 160 ASN H 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10570 Z= 0.174 Angle : 0.453 8.896 14227 Z= 0.253 Chirality : 0.036 0.155 1577 Planarity : 0.005 0.031 1711 Dihedral : 10.899 87.411 1731 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.98 % Allowed : 15.13 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.23), residues: 1239 helix: 2.45 (0.17), residues: 934 sheet: None (None), residues: 0 loop : -0.69 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 574 HIS 0.004 0.001 HIS E 60 PHE 0.022 0.001 PHE D 542 TYR 0.016 0.001 TYR G 200 ARG 0.004 0.000 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7685 (mmm160) cc_final: 0.7437 (mmm-85) REVERT: A 590 ARG cc_start: 0.8768 (mtt180) cc_final: 0.8312 (mpp-170) REVERT: A 623 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8637 (tt0) REVERT: B 623 GLU cc_start: 0.8255 (tt0) cc_final: 0.8037 (tt0) REVERT: B 809 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6955 (mt-10) REVERT: C 542 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7384 (p90) REVERT: C 590 ARG cc_start: 0.8875 (mtt180) cc_final: 0.8665 (mmt90) REVERT: C 623 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: D 590 ARG cc_start: 0.8842 (mpt-90) cc_final: 0.8129 (mtt90) REVERT: D 623 GLU cc_start: 0.8927 (tt0) cc_final: 0.8542 (mm-30) REVERT: D 809 GLU cc_start: 0.6623 (mm-30) cc_final: 0.6146 (mt-10) REVERT: E 10 MET cc_start: 0.8289 (tpp) cc_final: 0.7932 (tpt) REVERT: E 37 ARG cc_start: 0.8163 (mtp-110) cc_final: 0.7832 (mtp85) REVERT: E 56 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7549 (mm-30) REVERT: E 81 ASP cc_start: 0.8100 (m-30) cc_final: 0.7614 (t0) REVERT: E 131 ARG cc_start: 0.5308 (tpt90) cc_final: 0.4946 (mmm-85) REVERT: F 41 ARG cc_start: 0.5607 (ttt-90) cc_final: 0.5273 (ptp-170) REVERT: F 65 ARG cc_start: 0.7390 (mtm-85) cc_final: 0.6733 (mtp85) REVERT: F 150 ILE cc_start: 0.7763 (tt) cc_final: 0.7502 (pt) REVERT: G 65 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7625 (ptp90) REVERT: G 79 LYS cc_start: 0.8441 (ttmm) cc_final: 0.7932 (mptt) outliers start: 30 outliers final: 21 residues processed: 172 average time/residue: 1.4572 time to fit residues: 266.4571 Evaluate side-chains 179 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 120 optimal weight: 0.0570 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 58 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 198 HIS G 160 ASN H 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 10570 Z= 0.149 Angle : 0.437 7.990 14227 Z= 0.245 Chirality : 0.035 0.149 1577 Planarity : 0.005 0.031 1711 Dihedral : 10.711 86.897 1731 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.39 % Allowed : 15.62 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.23), residues: 1239 helix: 2.50 (0.17), residues: 934 sheet: None (None), residues: 0 loop : -0.66 (0.31), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 574 HIS 0.009 0.001 HIS H 204 PHE 0.027 0.001 PHE D 542 TYR 0.017 0.001 TYR G 200 ARG 0.004 0.000 ARG F 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7682 (mmm160) cc_final: 0.7439 (mmm-85) REVERT: A 590 ARG cc_start: 0.8776 (mtt180) cc_final: 0.8326 (mpp-170) REVERT: A 623 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8636 (tt0) REVERT: B 809 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6873 (mt-10) REVERT: C 542 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7432 (p90) REVERT: C 590 ARG cc_start: 0.8874 (mtt180) cc_final: 0.8666 (mmt90) REVERT: C 623 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: D 590 ARG cc_start: 0.8844 (mpt-90) cc_final: 0.8134 (mtt90) REVERT: D 623 GLU cc_start: 0.8930 (tt0) cc_final: 0.8505 (mm-30) REVERT: D 809 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6138 (mt-10) REVERT: E 37 ARG cc_start: 0.8169 (mtp-110) cc_final: 0.7832 (mtp85) REVERT: E 56 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7553 (mm-30) REVERT: E 81 ASP cc_start: 0.8086 (m-30) cc_final: 0.7621 (t0) REVERT: E 131 ARG cc_start: 0.5310 (tpt90) cc_final: 0.4950 (mmm-85) REVERT: F 41 ARG cc_start: 0.5607 (ttt-90) cc_final: 0.5273 (ptp-170) REVERT: F 65 ARG cc_start: 0.7390 (mtm-85) cc_final: 0.6748 (mtp85) REVERT: F 150 ILE cc_start: 0.7812 (tt) cc_final: 0.7557 (pt) REVERT: G 65 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7665 (ptp90) REVERT: G 79 LYS cc_start: 0.8422 (ttmm) cc_final: 0.7915 (mptt) outliers start: 24 outliers final: 19 residues processed: 170 average time/residue: 1.4327 time to fit residues: 258.8900 Evaluate side-chains 176 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 198 HIS G 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.084113 restraints weight = 52642.891| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.86 r_work: 0.2647 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 10570 Z= 0.148 Angle : 0.438 7.771 14227 Z= 0.244 Chirality : 0.035 0.137 1577 Planarity : 0.005 0.031 1711 Dihedral : 10.544 86.157 1731 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.59 % Allowed : 15.62 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.23), residues: 1239 helix: 2.52 (0.17), residues: 934 sheet: None (None), residues: 0 loop : -0.68 (0.31), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 574 HIS 0.003 0.001 HIS H 204 PHE 0.028 0.001 PHE D 542 TYR 0.017 0.001 TYR G 200 ARG 0.004 0.000 ARG E 65 =============================================================================== Job complete usr+sys time: 4496.44 seconds wall clock time: 80 minutes 14.74 seconds (4814.74 seconds total)