Starting phenix.real_space_refine on Thu Mar 14 23:16:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2h_16390/03_2024/8c2h_16390_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2h_16390/03_2024/8c2h_16390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2h_16390/03_2024/8c2h_16390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2h_16390/03_2024/8c2h_16390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2h_16390/03_2024/8c2h_16390_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2h_16390/03_2024/8c2h_16390_updated.pdb" } resolution = 2.64 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 2 5.49 5 S 61 5.16 5 C 6664 2.51 5 N 1558 2.21 5 O 1786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 541": "NH1" <-> "NH2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 566": "OE1" <-> "OE2" Residue "C PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C ARG 590": "NH1" <-> "NH2" Residue "C PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "F PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 31": "OD1" <-> "OD2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 92": "OD1" <-> "OD2" 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 "G PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 31": "OD1" <-> "OD2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 41": "NH1" <-> "NH2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "H PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 31": "OD1" <-> "OD2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 92": "OD1" <-> "OD2" 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" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10071 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1037 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 133, 1010 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 133, 1010 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 1009 Chain: "B" Number of atoms: 1071 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 134, 1025 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 134, 1025 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 1003 Chain: "C" Number of atoms: 1043 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 134, 1016 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 134, 1016 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 1015 Chain: "D" Number of atoms: 1120 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 141, 1083 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 141, 1083 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 1071 Chain: "E" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1354 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 3 Chain: "F" Number of atoms: 1365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 174, 1354 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 174, 1354 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 3 bond proxies already assigned to first conformer: 1373 Chain: "G" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1354 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 3 Chain: "H" Number of atoms: 1365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 174, 1354 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 174, 1354 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 2, 'TRANS': 171} Chain breaks: 3 bond proxies already assigned to first conformer: 1373 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 21 residue: pdb=" N AGLN A 583 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 583 " occ=0.50 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 B 570 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 570 " 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 AILE B 587 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE B 587 " occ=0.50 residue: pdb=" N AGLN C 583 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 583 " occ=0.50 residue: pdb=" N AGLY C 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY C 584 " occ=0.50 ... (remaining 9 not shown) Time building chain proxies: 9.27, per 1000 atoms: 0.92 Number of scatterers: 10071 At special positions: 0 Unit cell: (99.946, 97.468, 87.556, 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 61 16.00 P 2 15.00 O 1786 8.00 N 1558 7.00 C 6664 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=2.02 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.05 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.02 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.05 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=2.01 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.04 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: 4.56 Conformation dependent library (CDL) restraints added in 3.2 seconds 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2294 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 8 sheets defined 68.7% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 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 540 Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 592 through 620 removed outlier: 3.517A pdb=" N ALA A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 814 removed outlier: 5.110A pdb=" N GLY A 790 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 791 " --> pdb=" O ASN A 787 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (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 540 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 592 through 613 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 785 through 814 removed outlier: 5.162A pdb=" N GLY B 790 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 791 " --> 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 540 Processing helix chain 'C' and resid 569 through 580 Processing helix chain 'C' and resid 592 through 620 Processing helix chain 'C' and resid 785 through 814 removed outlier: 5.120A pdb=" N GLY C 790 " --> pdb=" O SER C 786 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 791 " --> pdb=" O ASN C 787 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (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 542 Processing helix chain 'D' and resid 569 through 580 Processing helix chain 'D' and resid 592 through 613 Processing helix chain 'D' and resid 616 through 620 Processing helix chain 'D' and resid 785 through 814 removed outlier: 5.126A pdb=" N GLY D 790 " --> pdb=" O SER D 786 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL D 791 " --> 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 104 Processing helix chain 'E' and resid 106 through 127 removed outlier: 3.889A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 160 removed outlier: 3.578A pdb=" N ILE E 157 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 206 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 127 removed outlier: 3.913A pdb=" N GLU F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 160 removed outlier: 3.593A pdb=" N ILE F 157 " --> pdb=" O ILE F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 206 Processing helix chain 'G' and resid 6 through 29 Processing helix chain 'G' and resid 93 through 104 Processing helix chain 'G' and resid 106 through 127 removed outlier: 3.891A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 160 removed outlier: 3.570A pdb=" N ILE G 157 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 206 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 127 removed outlier: 3.904A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 160 removed outlier: 3.589A pdb=" N ILE H 157 " --> pdb=" O ILE H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 206 Processing sheet with id= A, first strand: chain 'E' and resid 34 through 36 Processing sheet with id= B, first strand: chain 'E' and resid 59 through 61 Processing sheet with id= C, first strand: chain 'F' and resid 34 through 36 Processing sheet with id= D, first strand: chain 'F' and resid 59 through 61 Processing sheet with id= E, first strand: chain 'G' and resid 34 through 36 Processing sheet with id= F, first strand: chain 'G' and resid 59 through 61 Processing sheet with id= G, first strand: chain 'H' and resid 34 through 36 Processing sheet with id= H, first strand: chain 'H' and resid 59 through 61 697 hydrogen bonds defined for protein. 1793 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: 2.88 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1636 1.32 - 1.45: 3580 1.45 - 1.59: 4916 1.59 - 1.72: 4 1.72 - 1.85: 86 Bond restraints: 10222 Sorted by residual: bond pdb=" CG HIS F 60 " pdb=" CD2 HIS F 60 " ideal model delta sigma weight residual 1.354 1.320 0.034 1.10e-02 8.26e+03 9.40e+00 bond pdb=" C1 POV G 401 " pdb=" O11 POV G 401 " ideal model delta sigma weight residual 1.410 1.469 -0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" CA SER H 144 " pdb=" CB SER H 144 " ideal model delta sigma weight residual 1.528 1.482 0.046 1.56e-02 4.11e+03 8.80e+00 bond pdb=" C1 POV E 401 " pdb=" O11 POV E 401 " ideal model delta sigma weight residual 1.410 1.469 -0.059 2.00e-02 2.50e+03 8.71e+00 bond pdb=" CG HIS H 132 " pdb=" CD2 HIS H 132 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 8.06e+00 ... (remaining 10217 not shown) Histogram of bond angle deviations from ideal: 95.15 - 103.07: 37 103.07 - 110.99: 3003 110.99 - 118.91: 5266 118.91 - 126.83: 5351 126.83 - 134.75: 128 Bond angle restraints: 13785 Sorted by residual: angle pdb=" C ARG A 541 " pdb=" CA ARG A 541 " pdb=" CB ARG A 541 " ideal model delta sigma weight residual 111.95 101.14 10.81 1.45e+00 4.76e-01 5.55e+01 angle pdb=" N LEU F 69 " pdb=" CA LEU F 69 " pdb=" CB LEU F 69 " ideal model delta sigma weight residual 110.67 101.10 9.57 1.39e+00 5.18e-01 4.74e+01 angle pdb=" CA HIS H 132 " pdb=" CB HIS H 132 " pdb=" CG HIS H 132 " ideal model delta sigma weight residual 113.80 119.45 -5.65 1.00e+00 1.00e+00 3.19e+01 angle pdb=" CA ASP H 81 " pdb=" CB ASP H 81 " pdb=" CG ASP H 81 " ideal model delta sigma weight residual 112.60 117.27 -4.67 1.00e+00 1.00e+00 2.18e+01 angle pdb=" C ASP H 31 " pdb=" CA ASP H 31 " pdb=" CB ASP H 31 " ideal model delta sigma weight residual 111.45 103.46 7.99 1.72e+00 3.38e-01 2.16e+01 ... (remaining 13780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.43: 5524 30.43 - 60.86: 273 60.86 - 91.29: 16 91.29 - 121.72: 10 121.72 - 152.15: 2 Dihedral angle restraints: 5825 sinusoidal: 2240 harmonic: 3585 Sorted by residual: dihedral pdb=" CB CYS E 67 " pdb=" SG CYS E 67 " pdb=" SG CYS E 77 " pdb=" CB CYS E 77 " ideal model delta sinusoidal sigma weight residual -86.00 -32.34 -53.66 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CB CYS G 67 " pdb=" SG CYS G 67 " pdb=" SG CYS G 77 " pdb=" CB CYS G 77 " ideal model delta sinusoidal sigma weight residual -86.00 -32.56 -53.44 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CA AASP D 586 " pdb=" C AASP D 586 " pdb=" N AILE D 587 " pdb=" CA AILE D 587 " ideal model delta harmonic sigma weight residual -180.00 -150.74 -29.26 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 5822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 940 0.067 - 0.134: 473 0.134 - 0.200: 122 0.200 - 0.267: 16 0.267 - 0.334: 4 Chirality restraints: 1555 Sorted by residual: chirality pdb=" CA ARG G 37 " pdb=" N ARG G 37 " pdb=" C ARG G 37 " pdb=" CB ARG G 37 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA ARG E 37 " pdb=" N ARG E 37 " pdb=" C ARG E 37 " pdb=" CB ARG E 37 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA PHE D 542 " pdb=" N PHE D 542 " pdb=" C PHE D 542 " pdb=" CB PHE D 542 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 1552 not shown) Planarity restraints: 1663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 602 " 0.062 2.00e-02 2.50e+03 2.99e-02 2.23e+01 pdb=" CG TRP D 602 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP D 602 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP D 602 " -0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP D 602 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 602 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP D 602 " -0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 602 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 602 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP D 602 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 602 " -0.056 2.00e-02 2.50e+03 2.93e-02 2.15e+01 pdb=" CG TRP B 602 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP B 602 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 602 " 0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP B 602 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 602 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP B 602 " 0.028 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 602 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 602 " 0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP B 602 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 583 " -0.021 2.00e-02 2.50e+03 4.13e-02 1.70e+01 pdb=" C GLN D 583 " 0.071 2.00e-02 2.50e+03 pdb=" O GLN D 583 " -0.026 2.00e-02 2.50e+03 pdb=" N AGLY D 584 " -0.024 2.00e-02 2.50e+03 ... (remaining 1660 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2969 2.84 - 3.35: 10229 3.35 - 3.87: 17788 3.87 - 4.38: 19946 4.38 - 4.90: 33619 Nonbonded interactions: 84551 Sorted by model distance: nonbonded pdb=" ND1 HIS H 82 " pdb=" O HOH H1701 " model vdw 2.319 2.520 nonbonded pdb=" NH2 ARG A 541 " pdb=" O HOH A1501 " model vdw 2.319 2.520 nonbonded pdb=" NH1 ARG D 541 " pdb=" OE1 GLU D 566 " model vdw 2.349 2.520 nonbonded pdb=" N BASP A 586 " pdb=" OD1BASP A 586 " model vdw 2.350 2.520 nonbonded pdb=" NH1 ARG B 541 " pdb=" OE1 GLU B 566 " model vdw 2.353 2.520 ... (remaining 84546 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 569 or resid 571 through 582 or resid 588 thro \ ugh 815 or resid 1401 through 1402)) selection = (chain 'B' and ((resid 506 through 507 and (name N or name CA or name C or name \ O or name CB )) or resid 508 through 542 or resid 565 through 569 or resid 571 t \ hrough 582 or resid 588 through 622 or (resid 623 through 779 and (name N or nam \ e CA or name C or name O or name CB )) or resid 780 through 815 or (resid 1401 a \ nd (name CA or name CB or name C1 or name C2 or name C3 or name C4 or name C5 or \ name C6 or name C7 or name C8 or name C9 or name O1 or name O2 )) or resid 1402 \ )) selection = (chain 'C' and (resid 506 through 542 or resid 565 through 569 or resid 571 thro \ ugh 582 or resid 588 through 815 or resid 1401 through 1402)) selection = (chain 'D' and ((resid 506 through 507 and (name N or name CA or name C or name \ O or name CB )) or resid 508 through 542 or resid 565 through 569 or resid 571 t \ hrough 582 or resid 588 through 622 or (resid 623 and (name N or name CA or name \ C or name O or name CB )) or resid 779 through 815 or (resid 1401 and (name CA \ or name CB or name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or \ name C7 or name C8 or name C9 or name O1 or name O2 )) or resid 1402)) } ncs_group { reference = (chain 'E' and (resid 5 through 183 or resid 185 through 209)) selection = (chain 'F' and (resid 5 through 183 or resid 185 through 209)) selection = (chain 'G' and (resid 5 through 183 or resid 185 through 209)) selection = (chain 'H' and (resid 5 through 183 or resid 185 through 209)) } 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=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 6.200 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 37.060 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 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:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.009 0.068 10222 Z= 0.595 Angle : 1.447 10.807 13785 Z= 0.993 Chirality : 0.080 0.334 1555 Planarity : 0.010 0.100 1663 Dihedral : 17.608 152.149 3507 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 6.15 % Allowed : 6.35 % Favored : 87.50 % 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: -1.37 (0.21), residues: 1219 helix: -0.22 (0.15), residues: 899 sheet: -2.77 (0.58), residues: 60 loop : -2.46 (0.28), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.011 TRP D 602 HIS 0.012 0.003 HIS F 132 PHE 0.040 0.007 PHE C 575 TYR 0.036 0.008 TYR H 156 ARG 0.051 0.005 ARG A 541 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 140 time to evaluate : 1.122 Fit side-chains REVERT: A 542 PHE cc_start: 0.6531 (OUTLIER) cc_final: 0.5851 (p90) REVERT: A 566 GLU cc_start: 0.7086 (pp20) cc_final: 0.6842 (mm-30) REVERT: A 582 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: B 507 LYS cc_start: 0.6615 (ptpt) cc_final: 0.6286 (ptmm) REVERT: B 615 ASN cc_start: 0.7472 (m-40) cc_final: 0.7104 (t0) REVERT: B 803 MET cc_start: 0.8563 (mtp) cc_final: 0.8279 (mtp) REVERT: C 542 PHE cc_start: 0.4844 (OUTLIER) cc_final: 0.4469 (m-80) REVERT: C 581 MET cc_start: 0.9023 (mmt) cc_final: 0.8248 (mmt) REVERT: C 590 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8263 (mpp80) REVERT: C 804 LEU cc_start: 0.8034 (tp) cc_final: 0.7769 (tt) REVERT: D 566 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: D 623 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7392 (mt-10) REVERT: D 781 SER cc_start: 0.7967 (p) cc_final: 0.7709 (t) REVERT: E 31 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: E 41 ARG cc_start: 0.5258 (OUTLIER) cc_final: 0.5033 (ptm160) REVERT: E 184 PHE cc_start: 0.7436 (m-80) cc_final: 0.7177 (m-10) REVERT: F 37 ARG cc_start: 0.7046 (mtt-85) cc_final: 0.6762 (mtp85) REVERT: F 78 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6907 (pttp) REVERT: F 99 ARG cc_start: 0.7264 (mmp80) cc_final: 0.6549 (mtt90) REVERT: F 174 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8120 (p) REVERT: F 203 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6510 (mtpt) REVERT: F 207 LEU cc_start: 0.4579 (OUTLIER) cc_final: 0.4151 (pt) REVERT: G 31 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7264 (m-30) REVERT: H 24 MET cc_start: 0.8722 (tpt) cc_final: 0.7909 (tpt) REVERT: H 58 MET cc_start: 0.6513 (tpt) cc_final: 0.6043 (tmm) REVERT: H 79 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7808 (mtmm) REVERT: H 99 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6792 (mmm-85) REVERT: H 132 HIS cc_start: 0.6945 (OUTLIER) cc_final: 0.6522 (m-70) REVERT: H 174 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8311 (p) outliers start: 57 outliers final: 4 residues processed: 171 average time/residue: 1.1746 time to fit residues: 215.9978 Evaluate side-chains 133 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 590 ARG Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H 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: 0.9980 chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 160 ASN E 204 HIS G 160 ASN G 204 HIS H 132 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10222 Z= 0.171 Angle : 0.487 9.620 13785 Z= 0.274 Chirality : 0.036 0.146 1555 Planarity : 0.005 0.029 1663 Dihedral : 14.542 150.763 1621 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.17 % Allowed : 10.71 % Favored : 86.11 % 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: 1.72 (0.23), residues: 1219 helix: 2.09 (0.16), residues: 901 sheet: -0.41 (0.91), residues: 40 loop : -1.91 (0.30), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 602 HIS 0.003 0.001 HIS F 82 PHE 0.018 0.002 PHE C 570 TYR 0.010 0.001 TYR F 180 ARG 0.003 0.000 ARG F 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 542 PHE cc_start: 0.6403 (OUTLIER) cc_final: 0.5869 (p90) REVERT: B 507 LYS cc_start: 0.6551 (ptpt) cc_final: 0.6306 (ptmm) REVERT: B 590 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.7923 (mtt180) REVERT: B 615 ASN cc_start: 0.7415 (m-40) cc_final: 0.7020 (t0) REVERT: C 566 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7550 (mm-30) REVERT: C 581 MET cc_start: 0.8997 (mmt) cc_final: 0.8341 (mmt) REVERT: C 590 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.8267 (mpp80) REVERT: C 804 LEU cc_start: 0.8001 (tp) cc_final: 0.7783 (tt) REVERT: D 566 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7058 (pm20) REVERT: D 623 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7173 (mm-30) REVERT: E 37 ARG cc_start: 0.6838 (mtp-110) cc_final: 0.6636 (mtt-85) REVERT: E 41 ARG cc_start: 0.5304 (OUTLIER) cc_final: 0.5071 (ttm-80) REVERT: E 78 LYS cc_start: 0.6933 (tttt) cc_final: 0.6481 (ttpp) REVERT: E 184 PHE cc_start: 0.7450 (m-80) cc_final: 0.7212 (m-10) REVERT: E 202 GLU cc_start: 0.7148 (pt0) cc_final: 0.6919 (mt-10) REVERT: F 37 ARG cc_start: 0.6689 (mtt-85) cc_final: 0.6485 (mtp85) REVERT: F 65 ARG cc_start: 0.7373 (mtt90) cc_final: 0.7148 (mtm-85) REVERT: F 99 ARG cc_start: 0.7436 (mmp80) cc_final: 0.6727 (mtt90) REVERT: F 205 GLN cc_start: 0.6004 (mt0) cc_final: 0.5774 (mm-40) REVERT: G 31 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.6487 (m-30) REVERT: G 37 ARG cc_start: 0.7333 (ptp-110) cc_final: 0.7086 (ptp-110) REVERT: H 24 MET cc_start: 0.8512 (tpt) cc_final: 0.7907 (tpt) REVERT: H 58 MET cc_start: 0.6574 (tpt) cc_final: 0.6074 (tmm) REVERT: H 97 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7696 (mp) REVERT: H 99 ARG cc_start: 0.7539 (mmt-90) cc_final: 0.6864 (mmm-85) REVERT: H 132 HIS cc_start: 0.5823 (OUTLIER) cc_final: 0.5009 (m170) REVERT: H 172 SER cc_start: 0.6783 (t) cc_final: 0.6500 (p) REVERT: H 208 ARG cc_start: 0.4181 (OUTLIER) cc_final: 0.3647 (ptm160) outliers start: 27 outliers final: 8 residues processed: 152 average time/residue: 1.2634 time to fit residues: 205.7302 Evaluate side-chains 137 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 0.0060 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 ASN G 204 HIS H 149 ASN H 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10222 Z= 0.156 Angle : 0.458 9.540 13785 Z= 0.250 Chirality : 0.036 0.253 1555 Planarity : 0.004 0.029 1663 Dihedral : 12.539 141.303 1591 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.67 % Allowed : 11.21 % Favored : 85.12 % 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: 2.45 (0.23), residues: 1219 helix: 2.57 (0.17), residues: 901 sheet: None (None), residues: 0 loop : -1.32 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 602 HIS 0.003 0.001 HIS H 60 PHE 0.015 0.001 PHE C 570 TYR 0.010 0.001 TYR C 519 ARG 0.003 0.000 ARG F 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 1.060 Fit side-chains REVERT: A 542 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.6040 (p90) REVERT: B 507 LYS cc_start: 0.6391 (ptpt) cc_final: 0.6146 (ptmm) REVERT: B 511 PHE cc_start: 0.8756 (m-80) cc_final: 0.8530 (m-80) REVERT: B 590 ARG cc_start: 0.8318 (mmm-85) cc_final: 0.8008 (mtt180) REVERT: B 615 ASN cc_start: 0.7492 (m-40) cc_final: 0.7026 (t0) REVERT: B 807 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6575 (tp) REVERT: C 566 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7461 (mm-30) REVERT: C 581 MET cc_start: 0.8989 (mmt) cc_final: 0.8363 (mmt) REVERT: C 590 ARG cc_start: 0.8552 (mmm-85) cc_final: 0.8314 (mpp80) REVERT: C 804 LEU cc_start: 0.7975 (tp) cc_final: 0.7743 (tt) REVERT: D 566 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6900 (pm20) REVERT: D 625 MET cc_start: 0.7161 (tpp) cc_final: 0.6945 (mmt) REVERT: E 58 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6771 (tpt) REVERT: E 184 PHE cc_start: 0.7474 (m-80) cc_final: 0.7257 (m-10) REVERT: F 37 ARG cc_start: 0.6788 (mtt-85) cc_final: 0.6529 (mtp85) REVERT: F 65 ARG cc_start: 0.7388 (mtt90) cc_final: 0.7044 (mtm-85) REVERT: F 99 ARG cc_start: 0.7482 (mmp80) cc_final: 0.6755 (mtt90) REVERT: G 31 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.6556 (m-30) REVERT: G 37 ARG cc_start: 0.7291 (ptp-110) cc_final: 0.7087 (ptp-110) REVERT: H 24 MET cc_start: 0.8434 (tpt) cc_final: 0.7816 (tpt) REVERT: H 58 MET cc_start: 0.6603 (tpt) cc_final: 0.6049 (tmm) REVERT: H 97 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7670 (mp) REVERT: H 99 ARG cc_start: 0.7541 (mmt-90) cc_final: 0.6884 (mmm-85) REVERT: H 204 HIS cc_start: 0.6548 (OUTLIER) cc_final: 0.6234 (m90) REVERT: H 208 ARG cc_start: 0.4058 (OUTLIER) cc_final: 0.3630 (ptm160) outliers start: 32 outliers final: 14 residues processed: 147 average time/residue: 1.3059 time to fit residues: 205.6369 Evaluate side-chains 139 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 204 HIS 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 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 0.0970 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 204 HIS H 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 10222 Z= 0.146 Angle : 0.441 9.739 13785 Z= 0.238 Chirality : 0.035 0.209 1555 Planarity : 0.004 0.029 1663 Dihedral : 11.568 128.740 1587 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.27 % Allowed : 12.50 % Favored : 84.23 % 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: 2.56 (0.23), residues: 1219 helix: 2.61 (0.17), residues: 899 sheet: None (None), residues: 0 loop : -1.11 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 574 HIS 0.008 0.001 HIS H 204 PHE 0.013 0.001 PHE C 570 TYR 0.011 0.001 TYR H 200 ARG 0.006 0.000 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 1.158 Fit side-chains REVERT: A 542 PHE cc_start: 0.6533 (OUTLIER) cc_final: 0.6104 (p90) REVERT: B 507 LYS cc_start: 0.6393 (ptpt) cc_final: 0.6159 (ptmm) REVERT: B 511 PHE cc_start: 0.8790 (m-80) cc_final: 0.8570 (m-80) REVERT: B 590 ARG cc_start: 0.8319 (mmm-85) cc_final: 0.8017 (mtt180) REVERT: B 615 ASN cc_start: 0.7593 (m-40) cc_final: 0.7080 (t0) REVERT: B 807 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6568 (tp) REVERT: C 581 MET cc_start: 0.8972 (mmt) cc_final: 0.8417 (mmt) REVERT: C 590 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.8328 (mpp80) REVERT: C 804 LEU cc_start: 0.7982 (tp) cc_final: 0.7749 (tt) REVERT: D 566 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6927 (pm20) REVERT: E 58 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6603 (tpt) REVERT: E 184 PHE cc_start: 0.7483 (m-80) cc_final: 0.7257 (m-10) REVERT: F 37 ARG cc_start: 0.6869 (mtt-85) cc_final: 0.6618 (mtp85) REVERT: F 65 ARG cc_start: 0.7394 (mtt90) cc_final: 0.7089 (mtm-85) REVERT: F 99 ARG cc_start: 0.7491 (mmp80) cc_final: 0.6790 (mtt90) REVERT: G 31 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.6595 (m-30) REVERT: G 37 ARG cc_start: 0.7298 (ptp-110) cc_final: 0.6904 (mtp85) REVERT: H 24 MET cc_start: 0.8409 (tpt) cc_final: 0.7760 (tpt) REVERT: H 58 MET cc_start: 0.6548 (tpt) cc_final: 0.6153 (tmm) REVERT: H 97 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7683 (mp) REVERT: H 99 ARG cc_start: 0.7516 (mmt-90) cc_final: 0.6873 (mmm-85) REVERT: H 208 ARG cc_start: 0.4084 (OUTLIER) cc_final: 0.3652 (ptm160) outliers start: 28 outliers final: 18 residues processed: 141 average time/residue: 1.2857 time to fit residues: 194.2557 Evaluate side-chains 139 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 TYR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 204 HIS 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 25 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 149 ASN H 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10222 Z= 0.237 Angle : 0.518 10.201 13785 Z= 0.278 Chirality : 0.038 0.194 1555 Planarity : 0.004 0.028 1663 Dihedral : 11.627 115.863 1585 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.67 % Allowed : 12.50 % Favored : 83.83 % 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: 2.28 (0.23), residues: 1219 helix: 2.33 (0.16), residues: 899 sheet: None (None), residues: 0 loop : -0.95 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 64 HIS 0.005 0.001 HIS H 204 PHE 0.017 0.002 PHE C 570 TYR 0.016 0.002 TYR C 612 ARG 0.004 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 1.119 Fit side-chains REVERT: A 542 PHE cc_start: 0.6526 (OUTLIER) cc_final: 0.6217 (p90) REVERT: B 590 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.7955 (mtt180) REVERT: B 615 ASN cc_start: 0.7566 (m-40) cc_final: 0.7118 (t0) REVERT: B 807 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6621 (tp) REVERT: C 581 MET cc_start: 0.8994 (mmt) cc_final: 0.8437 (mmt) REVERT: C 590 ARG cc_start: 0.8556 (mmm-85) cc_final: 0.8333 (mpp80) REVERT: C 804 LEU cc_start: 0.8024 (tp) cc_final: 0.7791 (tt) REVERT: D 566 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: D 582 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: D 781 SER cc_start: 0.7979 (p) cc_final: 0.7709 (t) REVERT: E 76 VAL cc_start: 0.6939 (t) cc_final: 0.6689 (p) REVERT: E 78 LYS cc_start: 0.6756 (tttt) cc_final: 0.6556 (ttpp) REVERT: E 184 PHE cc_start: 0.7523 (m-80) cc_final: 0.7269 (m-10) REVERT: F 37 ARG cc_start: 0.7019 (mtt-85) cc_final: 0.6684 (mtp85) REVERT: F 99 ARG cc_start: 0.7433 (mmp80) cc_final: 0.6719 (mtt90) REVERT: F 208 ARG cc_start: 0.4792 (OUTLIER) cc_final: 0.4208 (mmm-85) REVERT: G 31 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.6824 (m-30) REVERT: G 37 ARG cc_start: 0.7394 (ptp-110) cc_final: 0.6972 (mtp85) REVERT: H 58 MET cc_start: 0.6610 (tpt) cc_final: 0.6146 (tmm) REVERT: H 97 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7626 (mp) REVERT: H 99 ARG cc_start: 0.7565 (mmt-90) cc_final: 0.6926 (mmm-85) REVERT: H 208 ARG cc_start: 0.4230 (OUTLIER) cc_final: 0.3771 (ptm160) outliers start: 32 outliers final: 14 residues processed: 138 average time/residue: 1.4104 time to fit residues: 207.7160 Evaluate side-chains 137 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 582 GLN Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 208 ARG Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 112 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 204 HIS G 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 10222 Z= 0.150 Angle : 0.442 10.183 13785 Z= 0.238 Chirality : 0.035 0.173 1555 Planarity : 0.004 0.029 1663 Dihedral : 10.584 108.189 1585 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.27 % Allowed : 13.29 % Favored : 83.43 % 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: 2.54 (0.23), residues: 1219 helix: 2.52 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -0.87 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 574 HIS 0.004 0.001 HIS E 204 PHE 0.012 0.001 PHE C 570 TYR 0.009 0.001 TYR C 519 ARG 0.005 0.000 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 1.148 Fit side-chains REVERT: A 542 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.6218 (p90) REVERT: B 590 ARG cc_start: 0.8339 (mmm-85) cc_final: 0.8031 (mtt180) REVERT: B 615 ASN cc_start: 0.7576 (m-40) cc_final: 0.7096 (t0) REVERT: B 807 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6544 (tp) REVERT: C 581 MET cc_start: 0.8988 (mmt) cc_final: 0.8389 (mmt) REVERT: C 590 ARG cc_start: 0.8560 (mmm-85) cc_final: 0.8346 (mpp80) REVERT: C 804 LEU cc_start: 0.8016 (tp) cc_final: 0.7784 (tt) REVERT: D 566 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6957 (pm20) REVERT: D 582 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8263 (mt0) REVERT: E 78 LYS cc_start: 0.6845 (tttt) cc_final: 0.6640 (ttpp) REVERT: E 184 PHE cc_start: 0.7490 (m-80) cc_final: 0.7268 (m-10) REVERT: F 37 ARG cc_start: 0.7099 (mtt-85) cc_final: 0.6773 (mtp85) REVERT: F 99 ARG cc_start: 0.7462 (mmp80) cc_final: 0.6709 (mtt90) REVERT: F 208 ARG cc_start: 0.4800 (OUTLIER) cc_final: 0.4253 (mmm-85) REVERT: G 31 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.6847 (m-30) REVERT: G 37 ARG cc_start: 0.7246 (ptp-110) cc_final: 0.6981 (mtp85) REVERT: H 58 MET cc_start: 0.6592 (tpt) cc_final: 0.6068 (tmm) REVERT: H 97 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7636 (mp) REVERT: H 99 ARG cc_start: 0.7517 (mmt-90) cc_final: 0.6863 (mmm-85) REVERT: H 132 HIS cc_start: 0.5503 (OUTLIER) cc_final: 0.4946 (p-80) REVERT: H 208 ARG cc_start: 0.4381 (OUTLIER) cc_final: 0.3850 (ptm160) outliers start: 28 outliers final: 16 residues processed: 133 average time/residue: 1.3589 time to fit residues: 192.7392 Evaluate side-chains 137 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 582 GLN Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 208 ARG Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10222 Z= 0.191 Angle : 0.473 10.179 13785 Z= 0.255 Chirality : 0.036 0.167 1555 Planarity : 0.004 0.029 1663 Dihedral : 10.670 104.568 1585 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.47 % Allowed : 13.49 % Favored : 83.04 % 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: 2.33 (0.23), residues: 1219 helix: 2.28 (0.16), residues: 917 sheet: None (None), residues: 0 loop : -0.83 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 64 HIS 0.004 0.001 HIS F 204 PHE 0.014 0.001 PHE C 570 TYR 0.013 0.001 TYR C 519 ARG 0.004 0.000 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 1.201 Fit side-chains REVERT: A 582 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7497 (mt0) REVERT: A 590 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8298 (mtp85) REVERT: B 590 ARG cc_start: 0.8327 (mmm-85) cc_final: 0.8011 (mtt180) REVERT: B 615 ASN cc_start: 0.7548 (m-40) cc_final: 0.7093 (t0) REVERT: B 807 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6548 (tp) REVERT: C 581 MET cc_start: 0.8995 (mmt) cc_final: 0.8445 (mmt) REVERT: C 590 ARG cc_start: 0.8545 (mmm-85) cc_final: 0.8327 (mpp80) REVERT: C 804 LEU cc_start: 0.7997 (tp) cc_final: 0.7765 (tt) REVERT: D 566 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7010 (pm20) REVERT: D 582 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8256 (mt0) REVERT: E 76 VAL cc_start: 0.6849 (t) cc_final: 0.6623 (p) REVERT: E 184 PHE cc_start: 0.7519 (m-80) cc_final: 0.7289 (m-10) REVERT: F 37 ARG cc_start: 0.7162 (mtt-85) cc_final: 0.6815 (mtp85) REVERT: F 99 ARG cc_start: 0.7456 (mmp80) cc_final: 0.6552 (mtp180) REVERT: F 205 GLN cc_start: 0.6008 (mt0) cc_final: 0.5716 (mp10) REVERT: F 208 ARG cc_start: 0.4722 (OUTLIER) cc_final: 0.4149 (mmm-85) REVERT: G 31 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.6947 (m-30) REVERT: G 37 ARG cc_start: 0.7289 (ptp-110) cc_final: 0.6863 (mtp85) REVERT: H 58 MET cc_start: 0.6603 (tpt) cc_final: 0.6077 (tmm) REVERT: H 97 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7609 (mp) REVERT: H 99 ARG cc_start: 0.7550 (mmt-90) cc_final: 0.6918 (mmm-85) REVERT: H 132 HIS cc_start: 0.5685 (OUTLIER) cc_final: 0.5010 (p-80) REVERT: H 208 ARG cc_start: 0.4474 (OUTLIER) cc_final: 0.3833 (ptm160) outliers start: 30 outliers final: 18 residues processed: 132 average time/residue: 1.3484 time to fit residues: 190.4736 Evaluate side-chains 141 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 582 GLN Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 208 ARG Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 111 optimal weight: 0.3980 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10222 Z= 0.208 Angle : 0.488 10.027 13785 Z= 0.262 Chirality : 0.037 0.159 1555 Planarity : 0.004 0.029 1663 Dihedral : 10.559 96.213 1583 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.57 % Allowed : 13.39 % Favored : 83.04 % 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: 2.24 (0.23), residues: 1219 helix: 2.23 (0.16), residues: 916 sheet: None (None), residues: 0 loop : -0.90 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 574 HIS 0.007 0.001 HIS F 204 PHE 0.014 0.001 PHE C 570 TYR 0.012 0.001 TYR C 612 ARG 0.004 0.000 ARG D 624 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.067 Fit side-chains REVERT: A 590 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8270 (mtp85) REVERT: B 615 ASN cc_start: 0.7542 (m-40) cc_final: 0.7087 (t0) REVERT: B 807 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6559 (tp) REVERT: C 581 MET cc_start: 0.8991 (mmt) cc_final: 0.8431 (mmt) REVERT: C 590 ARG cc_start: 0.8524 (mmm-85) cc_final: 0.8303 (mpp80) REVERT: C 804 LEU cc_start: 0.8002 (tp) cc_final: 0.7770 (tt) REVERT: D 566 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7040 (pm20) REVERT: D 582 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: E 76 VAL cc_start: 0.6712 (t) cc_final: 0.6509 (p) REVERT: E 184 PHE cc_start: 0.7530 (m-80) cc_final: 0.7281 (m-10) REVERT: F 37 ARG cc_start: 0.7187 (mtt-85) cc_final: 0.6873 (mtp85) REVERT: F 99 ARG cc_start: 0.7457 (mmp80) cc_final: 0.6577 (mtp180) REVERT: F 208 ARG cc_start: 0.4630 (OUTLIER) cc_final: 0.4190 (mmm-85) REVERT: G 31 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7175 (m-30) REVERT: G 120 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6306 (mp) REVERT: H 58 MET cc_start: 0.6648 (tpt) cc_final: 0.6135 (tmm) REVERT: H 97 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7603 (mp) REVERT: H 99 ARG cc_start: 0.7547 (mmt-90) cc_final: 0.6905 (mmm-85) REVERT: H 208 ARG cc_start: 0.4392 (OUTLIER) cc_final: 0.3740 (ptm160) outliers start: 31 outliers final: 20 residues processed: 138 average time/residue: 1.3320 time to fit residues: 196.5573 Evaluate side-chains 145 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 582 GLN Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 208 ARG Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10222 Z= 0.181 Angle : 0.472 9.972 13785 Z= 0.252 Chirality : 0.036 0.148 1555 Planarity : 0.004 0.029 1663 Dihedral : 10.161 85.712 1583 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.67 % Allowed : 13.39 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.23), residues: 1219 helix: 2.28 (0.16), residues: 916 sheet: None (None), residues: 0 loop : -0.90 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 574 HIS 0.006 0.001 HIS F 204 PHE 0.013 0.001 PHE C 570 TYR 0.011 0.001 TYR C 612 ARG 0.005 0.000 ARG D 624 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 1.100 Fit side-chains REVERT: A 582 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: A 590 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8268 (mtp85) REVERT: B 590 ARG cc_start: 0.8308 (mmm-85) cc_final: 0.7995 (mtt180) REVERT: B 615 ASN cc_start: 0.7532 (m-40) cc_final: 0.7070 (t0) REVERT: B 807 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6544 (tp) REVERT: C 581 MET cc_start: 0.8985 (mmt) cc_final: 0.8440 (mmt) REVERT: C 590 ARG cc_start: 0.8519 (mmm-85) cc_final: 0.8302 (mpp80) REVERT: C 804 LEU cc_start: 0.7990 (tp) cc_final: 0.7757 (tt) REVERT: D 566 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7033 (pm20) REVERT: D 582 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8255 (mt0) REVERT: E 184 PHE cc_start: 0.7527 (m-80) cc_final: 0.7286 (m-10) REVERT: F 37 ARG cc_start: 0.7187 (mtt-85) cc_final: 0.6881 (mtp85) REVERT: F 99 ARG cc_start: 0.7452 (mmp80) cc_final: 0.6570 (mtp180) REVERT: F 205 GLN cc_start: 0.5950 (mt0) cc_final: 0.5710 (mp10) REVERT: F 208 ARG cc_start: 0.4621 (OUTLIER) cc_final: 0.4143 (mmm-85) REVERT: G 31 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7287 (m-30) REVERT: H 58 MET cc_start: 0.6648 (tpt) cc_final: 0.6234 (tmm) REVERT: H 97 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7592 (mp) REVERT: H 99 ARG cc_start: 0.7568 (mmt-90) cc_final: 0.6932 (mmm-85) REVERT: H 208 ARG cc_start: 0.4411 (OUTLIER) cc_final: 0.3782 (ptm160) outliers start: 32 outliers final: 20 residues processed: 134 average time/residue: 1.3100 time to fit residues: 187.7397 Evaluate side-chains 141 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 582 GLN Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 208 ARG Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 76 optimal weight: 0.3980 chunk 102 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 204 HIS G 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10222 Z= 0.143 Angle : 0.443 9.685 13785 Z= 0.237 Chirality : 0.035 0.132 1555 Planarity : 0.004 0.029 1663 Dihedral : 9.614 82.398 1583 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.47 % Allowed : 13.59 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.23), residues: 1219 helix: 2.42 (0.17), residues: 917 sheet: None (None), residues: 0 loop : -0.86 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 177 HIS 0.005 0.001 HIS H 204 PHE 0.011 0.001 PHE C 570 TYR 0.009 0.001 TYR C 519 ARG 0.005 0.000 ARG D 624 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 1.039 Fit side-chains REVERT: A 590 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8268 (mtp85) REVERT: B 590 ARG cc_start: 0.8321 (mmm-85) cc_final: 0.8015 (mtt180) REVERT: B 615 ASN cc_start: 0.7518 (m-40) cc_final: 0.7040 (t0) REVERT: B 807 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6535 (tp) REVERT: C 581 MET cc_start: 0.8992 (mmt) cc_final: 0.8449 (mmt) REVERT: C 590 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8244 (mpp80) REVERT: C 804 LEU cc_start: 0.7996 (tp) cc_final: 0.7763 (tt) REVERT: D 566 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: D 582 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8265 (mt0) REVERT: E 184 PHE cc_start: 0.7513 (m-80) cc_final: 0.7293 (m-10) REVERT: F 37 ARG cc_start: 0.7208 (mtt-85) cc_final: 0.6835 (mtp85) REVERT: F 65 ARG cc_start: 0.7324 (mtt180) cc_final: 0.7063 (mtm-85) REVERT: F 99 ARG cc_start: 0.7444 (mmp80) cc_final: 0.6561 (mtp180) REVERT: F 208 ARG cc_start: 0.4562 (OUTLIER) cc_final: 0.4182 (mmm-85) REVERT: G 31 ASP cc_start: 0.7653 (m-30) cc_final: 0.7296 (m-30) REVERT: G 120 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6402 (mp) REVERT: H 58 MET cc_start: 0.6645 (tpt) cc_final: 0.6246 (tmm) REVERT: H 99 ARG cc_start: 0.7565 (mmt-90) cc_final: 0.6883 (mmm-85) REVERT: H 208 ARG cc_start: 0.4238 (OUTLIER) cc_final: 0.3656 (ptm160) outliers start: 30 outliers final: 21 residues processed: 131 average time/residue: 1.2921 time to fit residues: 181.2990 Evaluate side-chains 137 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 582 GLN Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 208 ARG Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 208 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.142749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.109621 restraints weight = 51660.281| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 5.72 r_work: 0.2484 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2452 r_free = 0.2452 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2452 r_free = 0.2452 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10222 Z= 0.158 Angle : 0.451 9.461 13785 Z= 0.241 Chirality : 0.035 0.134 1555 Planarity : 0.004 0.029 1663 Dihedral : 9.587 81.028 1581 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.17 % Allowed : 13.89 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.23), residues: 1219 helix: 2.40 (0.16), residues: 917 sheet: None (None), residues: 0 loop : -0.84 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 574 HIS 0.006 0.001 HIS H 204 PHE 0.012 0.001 PHE C 570 TYR 0.009 0.001 TYR C 519 ARG 0.005 0.000 ARG D 624 =============================================================================== Job complete usr+sys time: 3746.13 seconds wall clock time: 66 minutes 37.79 seconds (3997.79 seconds total)