Starting phenix.real_space_refine on Fri Nov 17 05:35:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8piv_17692/11_2023/8piv_17692_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8piv_17692/11_2023/8piv_17692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8piv_17692/11_2023/8piv_17692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8piv_17692/11_2023/8piv_17692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8piv_17692/11_2023/8piv_17692_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8piv_17692/11_2023/8piv_17692_updated.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.045 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 5 5.49 5 S 124 5.16 5 C 11892 2.51 5 N 2845 2.21 5 O 3223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 422": "OE1" <-> "OE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 638": "OD1" <-> "OD2" Residue "A ASP 651": "OD1" <-> "OD2" Residue "A ASP 668": "OD1" <-> "OD2" Residue "A GLU 710": "OE1" <-> "OE2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "A TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B GLU 550": "OE1" <-> "OE2" Residue "B PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 651": "OD1" <-> "OD2" Residue "B ASP 668": "OD1" <-> "OD2" Residue "B GLU 710": "OE1" <-> "OE2" Residue "C GLU 422": "OE1" <-> "OE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 590": "OD1" <-> "OD2" Residue "C PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 638": "OD1" <-> "OD2" Residue "C ASP 651": "OD1" <-> "OD2" Residue "C ASP 668": "OD1" <-> "OD2" Residue "C GLU 710": "OE1" <-> "OE2" Residue "C PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 422": "OE1" <-> "OE2" Residue "D ASP 427": "OD1" <-> "OD2" Residue "D ASP 447": "OD1" <-> "OD2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D GLU 487": "OE1" <-> "OE2" Residue "D PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 570": "OE1" <-> "OE2" Residue "D PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 638": "OD1" <-> "OD2" Residue "D ASP 651": "OD1" <-> "OD2" Residue "D ASP 668": "OD1" <-> "OD2" Residue "D PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 5": "OD1" <-> "OD2" Residue "E ASP 92": "OD1" <-> "OD2" Residue "E PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "F PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F ASP 92": "OD1" <-> "OD2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "F PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 18089 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3078 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3056 Classifications: {'peptide': 399} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 386} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 399, 3056 Classifications: {'peptide': 399} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 386} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 3096 Chain: "B" Number of atoms: 3027 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 395, 3016 Classifications: {'peptide': 395} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 383} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 395, 3016 Classifications: {'peptide': 395} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 383} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 3067 Chain: "C" Number of atoms: 3041 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 397, 3030 Classifications: {'peptide': 397} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 384} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Conformer: "B" Number of residues, atoms: 397, 3030 Classifications: {'peptide': 397} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 384} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 bond proxies already assigned to first conformer: 3084 Chain: "D" Number of atoms: 3018 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 393, 2996 Classifications: {'peptide': 393} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 381} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 393, 2996 Classifications: {'peptide': 393} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 381} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 3034 Chain: "E" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1373 Classifications: {'peptide': 177} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1382 Classifications: {'peptide': 178} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1373 Classifications: {'peptide': 177} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1370 Classifications: {'peptide': 177} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'OLC': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'PLM': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N APHE A 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 574 " occ=0.50 residue: pdb=" N APHE A 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 623 " occ=0.50 residue: pdb=" N APHE B 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.50 residue: pdb=" N APHE C 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 623 " occ=0.50 residue: pdb=" N APHE D 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 574 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.50 Time building chain proxies: 14.91, per 1000 atoms: 0.82 Number of scatterers: 18089 At special positions: 0 Unit cell: (115.64, 124.313, 137.323, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 P 5 15.00 O 3223 8.00 N 2845 7.00 C 11892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.04 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.06 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.04 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.05 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: 7.06 Conformation dependent library (CDL) restraints added in 5.7 seconds 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4150 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 21 sheets defined 53.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 523 through 545 Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 596 through 628 Processing helix chain 'A' and resid 636 through 640 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 665 through 676 removed outlier: 3.719A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 695 Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.548A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 removed outlier: 4.253A pdb=" N THR A 744 " --> pdb=" O SER A 741 " (cutoff:3.500A) Proline residue: A 745 - end of helix Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 793 through 819 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 417 through 420 Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 523 through 545 Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 596 through 624 Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 665 through 676 removed outlier: 3.670A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.541A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 755 Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 793 through 822 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 523 through 545 Processing helix chain 'C' and resid 548 through 550 No H-bonds generated for 'chain 'C' and resid 548 through 550' Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 596 through 625 Processing helix chain 'C' and resid 636 through 640 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 665 through 676 removed outlier: 3.720A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 695 Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.561A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 755 Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'C' and resid 793 through 820 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 523 through 544 Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.614A pdb=" N TRP D 578 " --> pdb=" O BPHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 625 Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 665 through 676 removed outlier: 3.617A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 708 through 714 Processing helix chain 'D' and resid 743 through 755 Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 793 through 822 Processing helix chain 'E' and resid 8 through 29 Processing helix chain 'E' and resid 93 through 103 Processing helix chain 'E' and resid 106 through 125 Processing helix chain 'E' and resid 134 through 161 removed outlier: 3.572A pdb=" N ALA E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 209 Processing helix chain 'F' and resid 6 through 27 Processing helix chain 'F' and resid 93 through 103 removed outlier: 3.565A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 126 removed outlier: 3.864A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 159 Processing helix chain 'F' and resid 178 through 208 Processing helix chain 'G' and resid 8 through 29 Processing helix chain 'G' and resid 93 through 103 Processing helix chain 'G' and resid 106 through 126 removed outlier: 4.044A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 160 Processing helix chain 'G' and resid 178 through 209 Processing helix chain 'H' and resid 6 through 29 removed outlier: 3.990A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 103 Processing helix chain 'H' and resid 106 through 125 Processing helix chain 'H' and resid 134 through 160 Processing helix chain 'H' and resid 178 through 209 Processing sheet with id= A, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= B, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= C, first strand: chain 'A' and resid 500 through 503 removed outlier: 6.354A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 494 through 498 removed outlier: 6.659A pdb=" N TYR A 732 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER A 497 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS A 730 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= F, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= G, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.034A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 494 through 498 removed outlier: 6.604A pdb=" N TYR B 732 " --> pdb=" O PHE B 495 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER B 497 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS B 730 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= J, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= K, first strand: chain 'C' and resid 720 through 723 removed outlier: 4.003A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.658A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= N, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= O, first strand: chain 'D' and resid 646 through 648 Processing sheet with id= P, first strand: chain 'D' and resid 494 through 498 removed outlier: 6.681A pdb=" N TYR D 732 " --> pdb=" O PHE D 495 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER D 497 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS D 730 " --> pdb=" O SER D 497 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 34 through 38 Processing sheet with id= R, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.829A pdb=" N LYS F 78 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 174 through 176 Processing sheet with id= T, first strand: chain 'H' and resid 36 through 38 Processing sheet with id= U, first strand: chain 'H' and resid 65 through 67 953 hydrogen bonds defined for protein. 2794 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: 5.82 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.52: 14694 1.52 - 1.88: 3769 1.88 - 2.24: 0 2.24 - 2.61: 0 2.61 - 2.97: 1 Bond restraints: 18464 Sorted by residual: bond pdb=" C PRO D 717 " pdb=" N ASP D 719 " ideal model delta sigma weight residual 1.332 2.966 -1.634 1.40e-02 5.10e+03 1.36e+04 bond pdb=" C SER C 785 " pdb=" O SER C 785 " ideal model delta sigma weight residual 1.235 1.162 0.073 1.26e-02 6.30e+03 3.36e+01 bond pdb=" N LEU B 624 " pdb=" CA LEU B 624 " ideal model delta sigma weight residual 1.458 1.397 0.060 1.29e-02 6.01e+03 2.18e+01 bond pdb=" N VAL B 488 " pdb=" CA VAL B 488 " ideal model delta sigma weight residual 1.456 1.498 -0.042 9.50e-03 1.11e+04 1.91e+01 bond pdb=" N VAL D 488 " pdb=" CA VAL D 488 " ideal model delta sigma weight residual 1.456 1.498 -0.041 9.50e-03 1.11e+04 1.88e+01 ... (remaining 18459 not shown) Histogram of bond angle deviations from ideal: 87.02 - 96.61: 1 96.61 - 106.19: 426 106.19 - 115.78: 11228 115.78 - 125.37: 12850 125.37 - 134.95: 340 Bond angle restraints: 24845 Sorted by residual: angle pdb=" O PRO D 717 " pdb=" C PRO D 717 " pdb=" N ASP D 719 " ideal model delta sigma weight residual 121.10 87.02 34.08 1.90e+00 2.77e-01 3.22e+02 angle pdb=" N ASP C 590 " pdb=" CA ASP C 590 " pdb=" C ASP C 590 " ideal model delta sigma weight residual 113.88 104.55 9.33 1.23e+00 6.61e-01 5.76e+01 angle pdb=" CA APHE B 623 " pdb=" C APHE B 623 " pdb=" N LEU B 624 " ideal model delta sigma weight residual 117.02 108.28 8.74 1.17e+00 7.31e-01 5.58e+01 angle pdb=" N CYS D 773 " pdb=" CA CYS D 773 " pdb=" C CYS D 773 " ideal model delta sigma weight residual 111.87 102.02 9.85 1.41e+00 5.03e-01 4.88e+01 angle pdb=" C APHE B 623 " pdb=" N LEU B 624 " pdb=" CA LEU B 624 " ideal model delta sigma weight residual 120.63 109.41 11.22 1.61e+00 3.86e-01 4.86e+01 ... (remaining 24840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.19: 9751 20.19 - 40.37: 770 40.37 - 60.56: 160 60.56 - 80.75: 29 80.75 - 100.93: 13 Dihedral angle restraints: 10723 sinusoidal: 4201 harmonic: 6522 Sorted by residual: dihedral pdb=" CA PRO D 717 " pdb=" C PRO D 717 " pdb=" N ASP D 719 " pdb=" CA ASP D 719 " ideal model delta harmonic sigma weight residual -180.00 -79.07 -100.93 0 5.00e+00 4.00e-02 4.07e+02 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 25.21 67.79 1 1.00e+01 1.00e-02 5.97e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual 93.00 36.95 56.05 1 1.00e+01 1.00e-02 4.24e+01 ... (remaining 10720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1511 0.088 - 0.177: 1067 0.177 - 0.265: 164 0.265 - 0.354: 20 0.354 - 0.442: 3 Chirality restraints: 2765 Sorted by residual: chirality pdb=" CG LEU D 498 " pdb=" CB LEU D 498 " pdb=" CD1 LEU D 498 " pdb=" CD2 LEU D 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CG LEU B 498 " pdb=" CB LEU B 498 " pdb=" CD1 LEU B 498 " pdb=" CD2 LEU B 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CB VAL D 746 " pdb=" CA VAL D 746 " pdb=" CG1 VAL D 746 " pdb=" CG2 VAL D 746 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 2762 not shown) Planarity restraints: 3012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 717 " 0.149 2.00e-02 2.50e+03 1.91e-01 3.63e+02 pdb=" C PRO D 717 " -0.325 2.00e-02 2.50e+03 pdb=" O PRO D 717 " 0.118 2.00e-02 2.50e+03 pdb=" N ASP D 719 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA APHE B 623 " -0.039 2.00e-02 2.50e+03 8.07e-02 6.51e+01 pdb=" C APHE B 623 " 0.139 2.00e-02 2.50e+03 pdb=" O APHE B 623 " -0.055 2.00e-02 2.50e+03 pdb=" N LEU B 624 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BPHE B 623 " -0.039 2.00e-02 2.50e+03 8.00e-02 6.40e+01 pdb=" C BPHE B 623 " 0.138 2.00e-02 2.50e+03 pdb=" O BPHE B 623 " -0.055 2.00e-02 2.50e+03 pdb=" N LEU B 624 " -0.045 2.00e-02 2.50e+03 ... (remaining 3009 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 435 2.68 - 3.24: 18239 3.24 - 3.79: 28346 3.79 - 4.35: 39956 4.35 - 4.90: 64075 Nonbonded interactions: 151051 Sorted by model distance: nonbonded pdb=" OG SER C 547 " pdb=" OE2 GLU C 550 " model vdw 2.127 2.440 nonbonded pdb=" O LYS E 129 " pdb=" OG1 THR E 130 " model vdw 2.217 2.440 nonbonded pdb=" O SER E 104 " pdb=" N ILE E 106 " model vdw 2.283 2.520 nonbonded pdb=" CZ APHE B 623 " pdb=" O SER C 785 " model vdw 2.285 3.340 nonbonded pdb=" OG SER A 592 " pdb=" OD2 ASP B 590 " model vdw 2.291 2.440 ... (remaining 151046 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 393 through 504 or (resid 505 through 506 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 through 573 or resid 575 t \ hrough 593 or (resid 594 and (name N or name CA or name C or name O or name CB ) \ ) or resid 595 through 622 or resid 624 through 626 or resid 633 or resid 635 or \ resid 637 or resid 639 through 709 or resid 711 through 717 or resid 721 throug \ h 812 or (resid 813 and (name N or name CA or name C or name O or name CB )) or \ resid 814 through 818 or (resid 819 through 823 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'B' and (resid 393 through 504 or (resid 505 through 506 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 or (resid 511 and (name N \ or name CA or name C or name O or name CB )) or resid 512 through 551 or (resid \ 569 and (name N or name CA or name C or name O or name CB )) or resid 570 throug \ h 573 or resid 575 or (resid 576 and (name N or name CA or name C or name O or n \ ame CB )) or resid 577 through 593 or (resid 594 and (name N or name CA or name \ C or name O or name CB )) or resid 595 through 622 or resid 624 through 626 or r \ esid 633 through 635 or resid 637 through 709 or resid 711 through 717 or resid \ 721 through 774 or (resid 784 and (name N or name CA or name C or name O or name \ CB )) or resid 785 through 823)) selection = (chain 'C' and (resid 393 through 504 or (resid 505 through 506 and (name N or n \ ame CA or name C or name O or name CB )) or resid 510 through 573 or resid 575 o \ r (resid 576 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 77 through 622 or resid 624 through 626 or resid 633 or resid 635 or resid 637 o \ r resid 639 through 709 or resid 711 through 717 or resid 721 through 812 or (re \ sid 813 and (name N or name CA or name C or name O or name CB )) or resid 814 th \ rough 818 or (resid 819 through 823 and (name N or name CA or name C or name O o \ r name CB )))) selection = (chain 'D' and (resid 393 through 510 or (resid 511 and (name N or name CA or na \ me C or name O or name CB )) or resid 512 through 551 or (resid 569 and (name N \ or name CA or name C or name O or name CB )) or resid 570 through 573 or resid 5 \ 75 or (resid 576 and (name N or name CA or name C or name O or name CB )) or res \ id 577 through 593 or (resid 594 and (name N or name CA or name C or name O or n \ ame CB )) or resid 595 through 622 or resid 624 through 633 or resid 635 through \ 637 or resid 639 through 717 or resid 721 through 774 or (resid 784 and (name N \ or name CA or name C or name O or name CB )) or resid 785 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 84 or resid 93 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 55 through 69 or (resid 70 and (name \ N or name CA or name C or name O or name CB )) or resid 71 through 84 or resid \ 93 through 210)) selection = (chain 'G' and (resid 5 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 84 or resid 93 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 through 210)) } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.500 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 58.040 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5148 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 : 0.017 1.634 18464 Z= 1.096 Angle : 1.484 34.082 24845 Z= 1.045 Chirality : 0.105 0.442 2765 Planarity : 0.014 0.267 3012 Dihedral : 15.285 100.932 6540 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.62 % Favored : 96.02 % Rotamer: Outliers : 1.59 % Allowed : 3.01 % Favored : 95.40 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2228 helix: 1.09 (0.14), residues: 1312 sheet: -1.92 (0.39), residues: 93 loop : -1.89 (0.19), residues: 823 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 350 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 373 average time/residue: 0.3783 time to fit residues: 197.8113 Evaluate side-chains 206 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 1.943 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2815 time to fit residues: 7.2250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.8980 chunk 169 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 203 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 587 GLN C 619 ASN E 79 GLN E 160 ASN F 160 ASN F 205 HIS H 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5184 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18464 Z= 0.186 Angle : 0.590 8.495 24845 Z= 0.306 Chirality : 0.041 0.217 2765 Planarity : 0.004 0.083 3012 Dihedral : 10.329 88.219 2739 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.94 % Favored : 97.88 % Rotamer: Outliers : 1.09 % Allowed : 10.89 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.23 (0.18), residues: 2230 helix: 2.30 (0.14), residues: 1302 sheet: -1.60 (0.37), residues: 153 loop : -1.33 (0.21), residues: 775 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 231 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 243 average time/residue: 0.3223 time to fit residues: 116.7682 Evaluate side-chains 191 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 183 time to evaluate : 1.938 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1571 time to fit residues: 4.8686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 0.2980 chunk 63 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 202 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN E 205 HIS F 132 HIS G 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5245 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18464 Z= 0.216 Angle : 0.555 9.061 24845 Z= 0.289 Chirality : 0.041 0.194 2765 Planarity : 0.004 0.072 3012 Dihedral : 9.645 87.345 2739 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.35 % Favored : 97.47 % Rotamer: Outliers : 1.26 % Allowed : 11.66 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.51 (0.18), residues: 2230 helix: 2.51 (0.14), residues: 1314 sheet: -1.49 (0.39), residues: 139 loop : -1.26 (0.21), residues: 777 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 220 average time/residue: 0.3155 time to fit residues: 104.6800 Evaluate side-chains 194 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 182 time to evaluate : 1.791 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1844 time to fit residues: 6.5560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5254 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18464 Z= 0.201 Angle : 0.556 14.448 24845 Z= 0.285 Chirality : 0.041 0.247 2765 Planarity : 0.004 0.064 3012 Dihedral : 9.119 89.860 2739 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.17 % Favored : 97.65 % Rotamer: Outliers : 1.31 % Allowed : 12.53 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.70 (0.18), residues: 2230 helix: 2.68 (0.15), residues: 1306 sheet: -1.55 (0.39), residues: 134 loop : -1.13 (0.21), residues: 790 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 198 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 212 average time/residue: 0.3288 time to fit residues: 105.9778 Evaluate side-chains 193 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 2.069 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1701 time to fit residues: 7.2590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 5.9990 chunk 122 optimal weight: 0.0050 chunk 3 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 0.0060 chunk 184 optimal weight: 0.6980 chunk 149 optimal weight: 0.0670 chunk 0 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.9550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5248 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18464 Z= 0.172 Angle : 0.539 9.587 24845 Z= 0.274 Chirality : 0.040 0.273 2765 Planarity : 0.003 0.063 3012 Dihedral : 8.633 86.888 2739 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.26 % Favored : 97.56 % Rotamer: Outliers : 0.82 % Allowed : 13.03 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.83 (0.18), residues: 2230 helix: 2.81 (0.15), residues: 1307 sheet: -1.61 (0.39), residues: 137 loop : -1.11 (0.21), residues: 786 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 210 average time/residue: 0.3255 time to fit residues: 103.8734 Evaluate side-chains 185 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 179 time to evaluate : 1.944 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1788 time to fit residues: 4.4871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN F 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5341 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18464 Z= 0.328 Angle : 0.622 13.740 24845 Z= 0.315 Chirality : 0.042 0.200 2765 Planarity : 0.004 0.057 3012 Dihedral : 9.154 87.271 2739 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.98 % Favored : 96.84 % Rotamer: Outliers : 1.48 % Allowed : 13.36 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.64 (0.18), residues: 2230 helix: 2.56 (0.15), residues: 1316 sheet: -1.67 (0.39), residues: 148 loop : -1.02 (0.22), residues: 766 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 191 average time/residue: 0.3264 time to fit residues: 94.1926 Evaluate side-chains 176 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 1.953 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1649 time to fit residues: 7.4242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 99 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN D 791 ASN G 160 ASN G 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5271 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18464 Z= 0.163 Angle : 0.577 10.125 24845 Z= 0.287 Chirality : 0.040 0.196 2765 Planarity : 0.003 0.059 3012 Dihedral : 8.522 84.798 2739 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.99 % Favored : 97.83 % Rotamer: Outliers : 0.49 % Allowed : 14.45 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.86 (0.19), residues: 2230 helix: 2.79 (0.15), residues: 1312 sheet: -1.53 (0.40), residues: 139 loop : -1.05 (0.22), residues: 779 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 185 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 190 average time/residue: 0.3280 time to fit residues: 93.9542 Evaluate side-chains 175 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 170 time to evaluate : 2.013 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1720 time to fit residues: 4.3175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 30.0000 chunk 41 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN F 132 HIS G 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5370 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 18464 Z= 0.356 Angle : 0.641 10.703 24845 Z= 0.325 Chirality : 0.043 0.168 2765 Planarity : 0.004 0.054 3012 Dihedral : 9.129 83.417 2739 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.12 % Favored : 96.70 % Rotamer: Outliers : 1.04 % Allowed : 14.45 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.64 (0.19), residues: 2230 helix: 2.54 (0.15), residues: 1310 sheet: -1.59 (0.42), residues: 123 loop : -1.02 (0.22), residues: 797 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 184 average time/residue: 0.3277 time to fit residues: 91.8452 Evaluate side-chains 174 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 164 time to evaluate : 2.005 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1761 time to fit residues: 5.9495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.5980 chunk 206 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 181 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN F 132 HIS H 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5307 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18464 Z= 0.184 Angle : 0.601 14.365 24845 Z= 0.293 Chirality : 0.040 0.169 2765 Planarity : 0.003 0.058 3012 Dihedral : 8.644 82.724 2739 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.08 % Favored : 97.74 % Rotamer: Outliers : 0.33 % Allowed : 15.22 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.85 (0.19), residues: 2230 helix: 2.81 (0.15), residues: 1302 sheet: -1.44 (0.43), residues: 130 loop : -1.10 (0.22), residues: 798 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 180 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 182 average time/residue: 0.3646 time to fit residues: 101.4508 Evaluate side-chains 169 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 2.269 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1613 time to fit residues: 3.2935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 619 ASN D 619 ASN G 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5313 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18464 Z= 0.202 Angle : 0.591 14.187 24845 Z= 0.293 Chirality : 0.040 0.156 2765 Planarity : 0.003 0.054 3012 Dihedral : 8.508 81.839 2739 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.49 % Favored : 97.33 % Rotamer: Outliers : 0.33 % Allowed : 15.54 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.83 (0.19), residues: 2230 helix: 2.78 (0.15), residues: 1302 sheet: -1.39 (0.43), residues: 129 loop : -1.09 (0.22), residues: 799 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4460 Ramachandran restraints generated. 2230 Oldfield, 0 Emsley, 2230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 170 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 173 average time/residue: 0.3636 time to fit residues: 97.6300 Evaluate side-chains 171 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 2.189 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1775 time to fit residues: 4.0462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 8.9990 chunk 189 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 177 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN F 132 HIS F 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.136778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.077849 restraints weight = 115465.369| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 6.46 r_work: 0.2825 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 18464 Z= 0.391 Angle : 0.683 13.737 24845 Z= 0.342 Chirality : 0.043 0.163 2765 Planarity : 0.004 0.055 3012 Dihedral : 8.986 78.613 2739 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.30 % Favored : 96.52 % Rotamer: Outliers : 0.33 % Allowed : 15.60 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.58 (0.19), residues: 2230 helix: 2.54 (0.15), residues: 1305 sheet: -1.56 (0.44), residues: 124 loop : -1.11 (0.22), residues: 801 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3850.14 seconds wall clock time: 70 minutes 59.30 seconds (4259.30 seconds total)