Starting phenix.real_space_refine on Sun Mar 17 06:27:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/03_2024/8bc3_15961_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/03_2024/8bc3_15961.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/03_2024/8bc3_15961_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/03_2024/8bc3_15961_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/03_2024/8bc3_15961_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/03_2024/8bc3_15961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/03_2024/8bc3_15961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/03_2024/8bc3_15961_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/03_2024/8bc3_15961_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 10540 2.51 5 N 2700 2.21 5 O 3590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "H ARG 14": "NH1" <-> "NH2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "E ARG 14": "NH1" <-> "NH2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 104": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "F ARG 14": "NH1" <-> "NH2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "G ARG 14": "NH1" <-> "NH2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "G GLU 104": "OE1" <-> "OE2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "I ARG 14": "NH1" <-> "NH2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 104": "OE1" <-> "OE2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "J ARG 14": "NH1" <-> "NH2" Residue "J GLU 94": "OE1" <-> "OE2" Residue "J GLU 104": "OE1" <-> "OE2" Residue "J GLU 140": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16880 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "H" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "I" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "J" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Time building chain proxies: 8.95, per 1000 atoms: 0.53 Number of scatterers: 16880 At special positions: 0 Unit cell: (116.1, 121.5, 81.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 3590 8.00 N 2700 7.00 C 10540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.73 Conformation dependent library (CDL) restraints added in 3.0 seconds 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 10 sheets defined 51.2% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'A' and resid 39 through 49 Processing helix chain 'A' and resid 69 through 82 removed outlier: 3.654A pdb=" N LEU A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 118 through 126 removed outlier: 4.016A pdb=" N GLN A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'H' and resid 10 through 19 Processing helix chain 'H' and resid 29 through 35 Processing helix chain 'H' and resid 39 through 49 Processing helix chain 'H' and resid 69 through 82 removed outlier: 3.654A pdb=" N LEU H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 105 Processing helix chain 'H' and resid 118 through 126 removed outlier: 4.016A pdb=" N GLN H 123 " --> pdb=" O SER H 119 " (cutoff:3.500A) Proline residue: H 124 - end of helix Processing helix chain 'H' and resid 137 through 141 Processing helix chain 'H' and resid 149 through 158 Processing helix chain 'H' and resid 173 through 182 Processing helix chain 'H' and resid 191 through 198 Processing helix chain 'H' and resid 201 through 215 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 39 through 49 Processing helix chain 'B' and resid 69 through 82 removed outlier: 3.654A pdb=" N LEU B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 118 through 126 removed outlier: 4.015A pdb=" N GLN B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 149 through 158 Processing helix chain 'B' and resid 173 through 182 Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 69 through 82 removed outlier: 3.655A pdb=" N LEU C 82 " --> pdb=" O LYS C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 118 through 126 removed outlier: 4.015A pdb=" N GLN C 123 " --> pdb=" O SER C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 137 through 141 Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 173 through 182 Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'D' and resid 10 through 19 Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 69 through 82 removed outlier: 3.654A pdb=" N LEU D 82 " --> pdb=" O LYS D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 118 through 126 removed outlier: 4.016A pdb=" N GLN D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Proline residue: D 124 - end of helix Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 149 through 158 Processing helix chain 'D' and resid 173 through 182 Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 201 through 215 Processing helix chain 'E' and resid 10 through 19 Processing helix chain 'E' and resid 29 through 35 Processing helix chain 'E' and resid 39 through 49 Processing helix chain 'E' and resid 69 through 82 removed outlier: 3.654A pdb=" N LEU E 82 " --> pdb=" O LYS E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 105 Processing helix chain 'E' and resid 118 through 126 removed outlier: 4.016A pdb=" N GLN E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 173 through 182 Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'F' and resid 10 through 19 Processing helix chain 'F' and resid 29 through 35 Processing helix chain 'F' and resid 39 through 49 Processing helix chain 'F' and resid 69 through 82 removed outlier: 3.654A pdb=" N LEU F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 105 Processing helix chain 'F' and resid 118 through 126 removed outlier: 4.015A pdb=" N GLN F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'F' and resid 149 through 158 Processing helix chain 'F' and resid 173 through 182 Processing helix chain 'F' and resid 191 through 198 Processing helix chain 'F' and resid 201 through 215 Processing helix chain 'G' and resid 10 through 19 Processing helix chain 'G' and resid 29 through 35 Processing helix chain 'G' and resid 39 through 49 Processing helix chain 'G' and resid 69 through 82 removed outlier: 3.655A pdb=" N LEU G 82 " --> pdb=" O LYS G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 105 Processing helix chain 'G' and resid 118 through 126 removed outlier: 4.016A pdb=" N GLN G 123 " --> pdb=" O SER G 119 " (cutoff:3.500A) Proline residue: G 124 - end of helix Processing helix chain 'G' and resid 137 through 141 Processing helix chain 'G' and resid 149 through 158 Processing helix chain 'G' and resid 173 through 182 Processing helix chain 'G' and resid 191 through 198 Processing helix chain 'G' and resid 201 through 215 Processing helix chain 'I' and resid 10 through 19 Processing helix chain 'I' and resid 29 through 35 Processing helix chain 'I' and resid 39 through 49 Processing helix chain 'I' and resid 69 through 82 removed outlier: 3.654A pdb=" N LEU I 82 " --> pdb=" O LYS I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 105 Processing helix chain 'I' and resid 118 through 126 removed outlier: 4.016A pdb=" N GLN I 123 " --> pdb=" O SER I 119 " (cutoff:3.500A) Proline residue: I 124 - end of helix Processing helix chain 'I' and resid 137 through 141 Processing helix chain 'I' and resid 149 through 158 Processing helix chain 'I' and resid 173 through 182 Processing helix chain 'I' and resid 191 through 198 Processing helix chain 'I' and resid 201 through 215 Processing helix chain 'J' and resid 10 through 19 Processing helix chain 'J' and resid 29 through 35 Processing helix chain 'J' and resid 39 through 49 Processing helix chain 'J' and resid 69 through 82 removed outlier: 3.654A pdb=" N LEU J 82 " --> pdb=" O LYS J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 105 Processing helix chain 'J' and resid 118 through 126 removed outlier: 4.016A pdb=" N GLN J 123 " --> pdb=" O SER J 119 " (cutoff:3.500A) Proline residue: J 124 - end of helix Processing helix chain 'J' and resid 137 through 141 Processing helix chain 'J' and resid 149 through 158 Processing helix chain 'J' and resid 173 through 182 Processing helix chain 'J' and resid 191 through 198 Processing helix chain 'J' and resid 201 through 215 Processing sheet with id= A, first strand: chain 'A' and resid 186 through 189 removed outlier: 6.501A pdb=" N LYS A 2 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS A 189 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE A 4 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY A 24 " --> pdb=" O LEU A 5 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 186 through 189 removed outlier: 6.501A pdb=" N LYS H 2 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS H 189 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE H 4 " --> pdb=" O CYS H 189 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY H 24 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 186 through 189 removed outlier: 6.501A pdb=" N LYS B 2 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS B 189 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE B 4 " --> pdb=" O CYS B 189 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY B 24 " --> pdb=" O LEU B 5 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 186 through 189 removed outlier: 6.501A pdb=" N LYS C 2 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS C 189 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE C 4 " --> pdb=" O CYS C 189 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY C 24 " --> pdb=" O LEU C 5 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 186 through 189 removed outlier: 6.501A pdb=" N LYS D 2 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS D 189 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE D 4 " --> pdb=" O CYS D 189 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY D 24 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 186 through 189 removed outlier: 6.502A pdb=" N LYS E 2 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS E 189 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE E 4 " --> pdb=" O CYS E 189 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY E 24 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 186 through 189 removed outlier: 6.502A pdb=" N LYS F 2 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS F 189 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE F 4 " --> pdb=" O CYS F 189 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY F 24 " --> pdb=" O LEU F 5 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 186 through 189 removed outlier: 6.501A pdb=" N LYS G 2 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS G 189 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE G 4 " --> pdb=" O CYS G 189 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY G 24 " --> pdb=" O LEU G 5 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 186 through 189 removed outlier: 6.501A pdb=" N LYS I 2 " --> pdb=" O VAL I 187 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N CYS I 189 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE I 4 " --> pdb=" O CYS I 189 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY I 24 " --> pdb=" O LEU I 5 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 186 through 189 removed outlier: 6.502A pdb=" N LYS J 2 " --> pdb=" O VAL J 187 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N CYS J 189 " --> pdb=" O LYS J 2 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE J 4 " --> pdb=" O CYS J 189 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY J 24 " --> pdb=" O LEU J 5 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 2040 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: 4.72 Time building geometry restraints manager: 7.24 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: 2775 1.32 - 1.45: 4685 1.45 - 1.58: 9210 1.58 - 1.71: 30 1.71 - 1.84: 70 Bond restraints: 16770 Sorted by residual: bond pdb=" O2 QC9 F 301 " pdb=" S13 QC9 F 301 " ideal model delta sigma weight residual 1.510 1.344 0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" O2 QC9 C 301 " pdb=" S13 QC9 C 301 " ideal model delta sigma weight residual 1.510 1.344 0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" O14 QC9 J 301 " pdb=" S13 QC9 J 301 " ideal model delta sigma weight residual 1.510 1.344 0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" O2 QC9 A 301 " pdb=" S13 QC9 A 301 " ideal model delta sigma weight residual 1.510 1.344 0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" O2 QC9 E 301 " pdb=" S13 QC9 E 301 " ideal model delta sigma weight residual 1.510 1.344 0.166 2.00e-02 2.50e+03 6.88e+01 ... (remaining 16765 not shown) Histogram of bond angle deviations from ideal: 98.26 - 106.43: 520 106.43 - 114.60: 9524 114.60 - 122.77: 9132 122.77 - 130.94: 3674 130.94 - 139.11: 70 Bond angle restraints: 22920 Sorted by residual: angle pdb=" C3 QC9 J 301 " pdb=" C12 QC9 J 301 " pdb=" S13 QC9 J 301 " ideal model delta sigma weight residual 109.47 139.11 -29.64 3.00e+00 1.11e-01 9.76e+01 angle pdb=" C3 QC9 H 301 " pdb=" C12 QC9 H 301 " pdb=" S13 QC9 H 301 " ideal model delta sigma weight residual 109.47 139.10 -29.63 3.00e+00 1.11e-01 9.75e+01 angle pdb=" C3 QC9 E 301 " pdb=" C12 QC9 E 301 " pdb=" S13 QC9 E 301 " ideal model delta sigma weight residual 109.47 139.10 -29.63 3.00e+00 1.11e-01 9.75e+01 angle pdb=" C3 QC9 D 301 " pdb=" C12 QC9 D 301 " pdb=" S13 QC9 D 301 " ideal model delta sigma weight residual 109.47 139.09 -29.62 3.00e+00 1.11e-01 9.75e+01 angle pdb=" C3 QC9 G 301 " pdb=" C12 QC9 G 301 " pdb=" S13 QC9 G 301 " ideal model delta sigma weight residual 109.47 139.08 -29.61 3.00e+00 1.11e-01 9.74e+01 ... (remaining 22915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.18: 9199 33.18 - 66.36: 431 66.36 - 99.54: 40 99.54 - 132.73: 0 132.73 - 165.91: 10 Dihedral angle restraints: 9680 sinusoidal: 3360 harmonic: 6320 Sorted by residual: dihedral pdb=" CD ARG B 126 " pdb=" NE ARG B 126 " pdb=" CZ ARG B 126 " pdb=" NH1 ARG B 126 " ideal model delta sinusoidal sigma weight residual 0.00 -40.64 40.64 1 1.00e+01 1.00e-02 2.32e+01 dihedral pdb=" CD ARG H 126 " pdb=" NE ARG H 126 " pdb=" CZ ARG H 126 " pdb=" NH1 ARG H 126 " ideal model delta sinusoidal sigma weight residual 0.00 -40.59 40.59 1 1.00e+01 1.00e-02 2.31e+01 dihedral pdb=" CD ARG J 126 " pdb=" NE ARG J 126 " pdb=" CZ ARG J 126 " pdb=" NH1 ARG J 126 " ideal model delta sinusoidal sigma weight residual 0.00 -40.58 40.58 1 1.00e+01 1.00e-02 2.31e+01 ... (remaining 9677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 2296 0.141 - 0.281: 304 0.281 - 0.422: 0 0.422 - 0.562: 10 0.562 - 0.703: 20 Chirality restraints: 2630 Sorted by residual: chirality pdb=" C1 QC9 E 301 " pdb=" C2 QC9 E 301 " pdb=" C4 QC9 E 301 " pdb=" O1 QC9 E 301 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" C1 QC9 I 301 " pdb=" C2 QC9 I 301 " pdb=" C4 QC9 I 301 " pdb=" O1 QC9 I 301 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" C1 QC9 D 301 " pdb=" C2 QC9 D 301 " pdb=" C4 QC9 D 301 " pdb=" O1 QC9 D 301 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 2627 not shown) Planarity restraints: 2950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 126 " 0.703 9.50e-02 1.11e+02 3.15e-01 6.04e+01 pdb=" NE ARG B 126 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG B 126 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 126 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 126 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 126 " 0.703 9.50e-02 1.11e+02 3.15e-01 6.04e+01 pdb=" NE ARG F 126 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG F 126 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG F 126 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 126 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 126 " -0.702 9.50e-02 1.11e+02 3.15e-01 6.03e+01 pdb=" NE ARG G 126 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG G 126 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG G 126 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 126 " -0.021 2.00e-02 2.50e+03 ... (remaining 2947 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4415 2.83 - 3.35: 18662 3.35 - 3.86: 32720 3.86 - 4.38: 40283 4.38 - 4.90: 60104 Nonbonded interactions: 156184 Sorted by model distance: nonbonded pdb=" O LEU J 170 " pdb=" O HOH J 401 " model vdw 2.310 2.440 nonbonded pdb=" O LEU D 170 " pdb=" O HOH D 401 " model vdw 2.311 2.440 nonbonded pdb=" O LEU C 170 " pdb=" O HOH C 401 " model vdw 2.311 2.440 nonbonded pdb=" O LEU E 170 " pdb=" O HOH E 401 " model vdw 2.311 2.440 nonbonded pdb=" O LEU G 170 " pdb=" O HOH G 401 " model vdw 2.311 2.440 ... (remaining 156179 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 8.460 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 45.140 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.160 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:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 0.014 0.166 16770 Z= 0.931 Angle : 2.072 29.640 22920 Z= 1.348 Chirality : 0.114 0.703 2630 Planarity : 0.020 0.315 2950 Dihedral : 19.401 165.908 5600 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 11.95 % Allowed : 11.45 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.13), residues: 2130 helix: -2.78 (0.10), residues: 1300 sheet: -2.96 (0.20), residues: 300 loop : -2.03 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 214 HIS 0.004 0.001 HIS F 200 PHE 0.010 0.002 PHE F 131 TYR 0.019 0.002 TYR F 15 ARG 0.003 0.001 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 463 time to evaluate : 2.051 Fit side-chains REVERT: A 150 GLN cc_start: 0.8239 (tp40) cc_final: 0.7992 (tp-100) REVERT: H 122 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8143 (tt) REVERT: B 62 ILE cc_start: 0.8411 (pt) cc_final: 0.8160 (pt) REVERT: C 122 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8128 (tt) REVERT: D 62 ILE cc_start: 0.8416 (pt) cc_final: 0.8173 (pt) REVERT: E 162 ASN cc_start: 0.7692 (m-40) cc_final: 0.7480 (m110) REVERT: F 62 ILE cc_start: 0.8495 (pt) cc_final: 0.8146 (pt) REVERT: F 122 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8347 (tt) REVERT: I 62 ILE cc_start: 0.8498 (pt) cc_final: 0.8151 (pt) REVERT: I 122 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8320 (tt) REVERT: J 150 GLN cc_start: 0.8165 (tp40) cc_final: 0.7910 (mm-40) outliers start: 190 outliers final: 9 residues processed: 530 average time/residue: 1.3383 time to fit residues: 783.2896 Evaluate side-chains 303 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 290 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain I residue 83 SER Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 122 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.5980 chunk 159 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 190 optimal weight: 0.9990 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 63 ASN A 120 GLN A 141 ASN A 172 ASN A 175 GLN A 200 HIS H 63 ASN H 120 GLN H 141 ASN H 150 GLN H 172 ASN H 175 GLN H 199 GLN H 200 HIS H 216 ASN B 111 ASN B 172 ASN B 175 GLN B 200 HIS B 216 ASN C 63 ASN C 120 GLN C 141 ASN C 150 GLN C 172 ASN C 175 GLN C 199 GLN C 200 HIS C 216 ASN D 111 ASN D 172 ASN D 175 GLN D 200 HIS D 216 ASN E 111 ASN E 120 GLN E 141 ASN E 150 GLN E 172 ASN E 175 GLN E 200 HIS F 111 ASN F 120 GLN F 172 ASN F 175 GLN F 200 HIS G 31 HIS G 111 ASN G 120 GLN G 141 ASN G 150 GLN G 172 ASN G 175 GLN G 200 HIS I 111 ASN I 120 GLN I 172 ASN I 175 GLN I 200 HIS J 63 ASN J 120 GLN J 141 ASN J 172 ASN J 175 GLN J 200 HIS Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16770 Z= 0.183 Angle : 0.524 5.536 22920 Z= 0.280 Chirality : 0.044 0.146 2630 Planarity : 0.006 0.072 2950 Dihedral : 11.603 134.007 2373 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.45 % Allowed : 14.84 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2130 helix: 0.44 (0.13), residues: 1300 sheet: -1.30 (0.26), residues: 300 loop : -1.26 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 214 HIS 0.008 0.002 HIS G 200 PHE 0.010 0.002 PHE H 198 TYR 0.011 0.001 TYR B 205 ARG 0.003 0.001 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 284 time to evaluate : 2.004 Fit side-chains REVERT: A 6 ASP cc_start: 0.8213 (t0) cc_final: 0.7964 (t0) REVERT: H 62 ILE cc_start: 0.8360 (pt) cc_final: 0.8146 (pp) REVERT: H 122 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8471 (tt) REVERT: C 62 ILE cc_start: 0.8351 (pt) cc_final: 0.8142 (pp) REVERT: C 122 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8434 (tt) REVERT: F 62 ILE cc_start: 0.8403 (pt) cc_final: 0.8013 (pt) REVERT: F 130 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8021 (tptp) REVERT: I 62 ILE cc_start: 0.8407 (pt) cc_final: 0.8019 (pt) REVERT: I 171 ARG cc_start: 0.8450 (mmt-90) cc_final: 0.8247 (mmt-90) REVERT: J 6 ASP cc_start: 0.8167 (t0) cc_final: 0.7907 (t0) outliers start: 23 outliers final: 7 residues processed: 294 average time/residue: 1.6983 time to fit residues: 542.2941 Evaluate side-chains 282 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 272 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain J residue 122 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 170 optimal weight: 0.0270 chunk 189 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 150 GLN H 85 ASN H 150 GLN B 85 ASN B 150 GLN C 85 ASN C 150 GLN D 85 ASN D 150 GLN E 85 ASN E 150 GLN F 85 ASN G 65 HIS G 85 ASN G 150 GLN I 85 ASN J 85 ASN J 150 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16770 Z= 0.151 Angle : 0.465 5.298 22920 Z= 0.245 Chirality : 0.043 0.125 2630 Planarity : 0.004 0.041 2950 Dihedral : 10.949 126.862 2366 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.13 % Allowed : 12.52 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.17), residues: 2130 helix: 1.49 (0.14), residues: 1310 sheet: -0.79 (0.27), residues: 300 loop : -0.80 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 214 HIS 0.004 0.001 HIS G 65 PHE 0.008 0.001 PHE G 191 TYR 0.011 0.001 TYR F 205 ARG 0.002 0.000 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 278 time to evaluate : 1.946 Fit side-chains REVERT: A 6 ASP cc_start: 0.8231 (t0) cc_final: 0.7986 (t0) REVERT: H 62 ILE cc_start: 0.8350 (pt) cc_final: 0.8108 (pp) REVERT: H 151 ASP cc_start: 0.7948 (m-30) cc_final: 0.7734 (m-30) REVERT: H 171 ARG cc_start: 0.8549 (mmt-90) cc_final: 0.8060 (mpt90) REVERT: B 101 LYS cc_start: 0.8420 (tttm) cc_final: 0.8214 (ttpp) REVERT: C 62 ILE cc_start: 0.8368 (pt) cc_final: 0.8119 (pp) REVERT: C 151 ASP cc_start: 0.7926 (m-30) cc_final: 0.7726 (m-30) REVERT: C 171 ARG cc_start: 0.8547 (mmt-90) cc_final: 0.8059 (mpt90) REVERT: E 30 ARG cc_start: 0.8394 (ttp80) cc_final: 0.8064 (ttp-170) REVERT: F 130 LYS cc_start: 0.8252 (tptm) cc_final: 0.8022 (tptp) REVERT: I 160 ASN cc_start: 0.7800 (m-40) cc_final: 0.7587 (t0) REVERT: J 6 ASP cc_start: 0.8206 (t0) cc_final: 0.7975 (t0) REVERT: J 94 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7197 (tp30) outliers start: 18 outliers final: 7 residues processed: 290 average time/residue: 1.6825 time to fit residues: 528.3743 Evaluate side-chains 278 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 270 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 122 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN E 150 GLN G 150 GLN J 111 ASN J 150 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 0.035 16770 Z= 0.221 Angle : 0.523 5.284 22920 Z= 0.279 Chirality : 0.047 0.132 2630 Planarity : 0.005 0.044 2950 Dihedral : 11.075 135.093 2362 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.38 % Allowed : 11.38 % Favored : 87.23 % 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: 1.13 (0.17), residues: 2130 helix: 1.66 (0.14), residues: 1300 sheet: -0.75 (0.26), residues: 320 loop : -0.44 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 214 HIS 0.006 0.001 HIS J 65 PHE 0.011 0.002 PHE A 202 TYR 0.011 0.001 TYR G 205 ARG 0.003 0.000 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 283 time to evaluate : 1.726 Fit side-chains REVERT: A 94 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7233 (tp30) REVERT: H 62 ILE cc_start: 0.8316 (pt) cc_final: 0.8059 (pp) REVERT: H 171 ARG cc_start: 0.8571 (mmt-90) cc_final: 0.8053 (mpt90) REVERT: H 174 LYS cc_start: 0.8370 (tmmt) cc_final: 0.7947 (tmtm) REVERT: B 94 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7113 (tp30) REVERT: B 174 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7994 (tmmt) REVERT: C 62 ILE cc_start: 0.8319 (pt) cc_final: 0.8059 (pp) REVERT: C 171 ARG cc_start: 0.8566 (mmt-90) cc_final: 0.8048 (mpt90) REVERT: C 174 LYS cc_start: 0.8384 (tmmt) cc_final: 0.7955 (tmtm) REVERT: D 94 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7104 (tp30) REVERT: D 174 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.7999 (tmmt) REVERT: E 6 ASP cc_start: 0.8232 (t0) cc_final: 0.7960 (t70) REVERT: E 94 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7288 (tp30) REVERT: F 160 ASN cc_start: 0.7803 (m-40) cc_final: 0.7589 (t0) REVERT: G 6 ASP cc_start: 0.8251 (t0) cc_final: 0.7986 (t70) REVERT: G 94 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7288 (tp30) REVERT: I 160 ASN cc_start: 0.7809 (m-40) cc_final: 0.7591 (t0) REVERT: J 94 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7209 (tp30) outliers start: 22 outliers final: 4 residues processed: 291 average time/residue: 1.7270 time to fit residues: 545.0034 Evaluate side-chains 284 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 272 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 174 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain J residue 94 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 173 optimal weight: 0.0040 chunk 140 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN E 150 GLN G 150 GLN J 150 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16770 Z= 0.153 Angle : 0.457 5.310 22920 Z= 0.242 Chirality : 0.044 0.124 2630 Planarity : 0.004 0.032 2950 Dihedral : 10.320 128.925 2358 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.26 % Allowed : 11.32 % Favored : 87.42 % 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: 1.54 (0.18), residues: 2130 helix: 1.95 (0.14), residues: 1300 sheet: -0.48 (0.27), residues: 300 loop : -0.29 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 214 HIS 0.003 0.001 HIS A 65 PHE 0.008 0.001 PHE H 191 TYR 0.011 0.001 TYR A 205 ARG 0.001 0.000 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 281 time to evaluate : 1.745 Fit side-chains REVERT: A 94 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7091 (tp30) REVERT: A 130 LYS cc_start: 0.8358 (tttm) cc_final: 0.8133 (tttp) REVERT: H 62 ILE cc_start: 0.8340 (pt) cc_final: 0.8092 (pp) REVERT: H 171 ARG cc_start: 0.8556 (mmt-90) cc_final: 0.8036 (mpt90) REVERT: H 174 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7913 (tmmt) REVERT: B 94 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7014 (tp30) REVERT: B 174 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7925 (tmmt) REVERT: C 40 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7813 (mm) REVERT: C 62 ILE cc_start: 0.8349 (pt) cc_final: 0.8098 (pp) REVERT: C 171 ARG cc_start: 0.8551 (mmt-90) cc_final: 0.8028 (mpt90) REVERT: C 174 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7974 (tmtm) REVERT: D 94 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7005 (tp30) REVERT: D 174 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7919 (tmmt) REVERT: E 30 ARG cc_start: 0.8412 (ttp80) cc_final: 0.8060 (ttp-170) REVERT: E 94 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7120 (tp30) REVERT: G 94 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7120 (tp30) REVERT: I 160 ASN cc_start: 0.7873 (m-40) cc_final: 0.7663 (t0) REVERT: J 94 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7071 (tp30) outliers start: 20 outliers final: 5 residues processed: 286 average time/residue: 1.7441 time to fit residues: 539.5912 Evaluate side-chains 290 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 274 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 174 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain J residue 94 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 0.0870 chunk 203 optimal weight: 0.0040 chunk 168 optimal weight: 7.9990 chunk 94 optimal weight: 0.4980 chunk 16 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 overall best weight: 0.7172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN E 150 GLN G 150 GLN J 150 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16770 Z= 0.157 Angle : 0.461 5.305 22920 Z= 0.244 Chirality : 0.044 0.124 2630 Planarity : 0.004 0.032 2950 Dihedral : 10.037 126.884 2358 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.45 % Allowed : 10.63 % Favored : 87.92 % 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: 1.58 (0.18), residues: 2130 helix: 2.03 (0.14), residues: 1300 sheet: -0.57 (0.24), residues: 360 loop : -0.28 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 214 HIS 0.003 0.001 HIS J 65 PHE 0.008 0.001 PHE G 191 TYR 0.009 0.001 TYR B 205 ARG 0.001 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 278 time to evaluate : 1.765 Fit side-chains REVERT: A 130 LYS cc_start: 0.8402 (tttm) cc_final: 0.8175 (tttp) REVERT: H 62 ILE cc_start: 0.8327 (pt) cc_final: 0.8082 (pp) REVERT: H 171 ARG cc_start: 0.8571 (mmt-90) cc_final: 0.8030 (mpt90) REVERT: H 174 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7913 (tmmt) REVERT: B 94 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6991 (tp30) REVERT: B 108 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7936 (mp) REVERT: B 174 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7916 (tmmt) REVERT: B 196 GLU cc_start: 0.7576 (mp0) cc_final: 0.7352 (mm-30) REVERT: C 62 ILE cc_start: 0.8342 (pt) cc_final: 0.8090 (pp) REVERT: C 171 ARG cc_start: 0.8563 (mmt-90) cc_final: 0.8026 (mpt90) REVERT: C 174 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7918 (tmmt) REVERT: D 94 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6985 (tp30) REVERT: D 108 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7951 (mp) REVERT: D 174 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7915 (tmmt) REVERT: D 196 GLU cc_start: 0.7600 (mp0) cc_final: 0.7359 (mm-30) REVERT: E 6 ASP cc_start: 0.8177 (t0) cc_final: 0.7945 (t70) REVERT: E 94 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7088 (tp30) REVERT: E 174 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7998 (tmmt) REVERT: F 130 LYS cc_start: 0.8269 (tttm) cc_final: 0.8015 (tttp) REVERT: G 6 ASP cc_start: 0.8151 (t0) cc_final: 0.7948 (t0) REVERT: G 94 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7086 (tp30) REVERT: I 160 ASN cc_start: 0.7881 (m-40) cc_final: 0.7655 (t0) outliers start: 23 outliers final: 5 residues processed: 285 average time/residue: 1.7567 time to fit residues: 541.5973 Evaluate side-chains 292 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 276 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 174 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 122 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 113 optimal weight: 0.5980 chunk 202 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN E 150 GLN G 150 GLN J 150 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16770 Z= 0.208 Angle : 0.504 5.306 22920 Z= 0.269 Chirality : 0.046 0.132 2630 Planarity : 0.004 0.032 2950 Dihedral : 10.362 133.940 2358 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.38 % Allowed : 10.82 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.18), residues: 2130 helix: 1.93 (0.14), residues: 1300 sheet: -0.57 (0.26), residues: 320 loop : -0.24 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 214 HIS 0.005 0.001 HIS A 65 PHE 0.009 0.001 PHE E 191 TYR 0.011 0.001 TYR G 205 ARG 0.002 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 279 time to evaluate : 2.055 Fit side-chains REVERT: A 130 LYS cc_start: 0.8415 (tttm) cc_final: 0.8184 (tttp) REVERT: H 62 ILE cc_start: 0.8307 (pt) cc_final: 0.8053 (pp) REVERT: H 94 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6988 (tp30) REVERT: H 171 ARG cc_start: 0.8572 (mmt-90) cc_final: 0.8026 (mpt90) REVERT: H 174 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7958 (tmtm) REVERT: B 94 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7042 (tp30) REVERT: B 108 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7996 (mp) REVERT: B 174 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7955 (tmmt) REVERT: C 62 ILE cc_start: 0.8326 (pt) cc_final: 0.8066 (pp) REVERT: C 94 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6948 (tp30) REVERT: C 171 ARG cc_start: 0.8566 (mmt-90) cc_final: 0.8024 (mpt90) REVERT: C 174 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7973 (tmtm) REVERT: D 94 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7003 (tp30) REVERT: D 174 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7992 (tmmt) REVERT: D 196 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7410 (mm-30) REVERT: E 6 ASP cc_start: 0.8244 (t0) cc_final: 0.8023 (t70) REVERT: E 94 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7199 (tp30) REVERT: E 174 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8001 (tmmt) REVERT: F 130 LYS cc_start: 0.8276 (tttm) cc_final: 0.8018 (tttp) REVERT: G 6 ASP cc_start: 0.8243 (t0) cc_final: 0.8034 (t0) REVERT: G 94 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7194 (tp30) REVERT: G 174 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8006 (tmmt) REVERT: I 160 ASN cc_start: 0.7881 (m-40) cc_final: 0.7663 (t0) outliers start: 22 outliers final: 4 residues processed: 284 average time/residue: 1.7743 time to fit residues: 545.0702 Evaluate side-chains 293 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 275 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 174 LYS Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 174 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 18 optimal weight: 0.0170 chunk 159 optimal weight: 0.1980 chunk 184 optimal weight: 3.9990 overall best weight: 1.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 GLN J 150 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16770 Z= 0.255 Angle : 0.545 5.319 22920 Z= 0.294 Chirality : 0.048 0.132 2630 Planarity : 0.005 0.037 2950 Dihedral : 10.762 141.174 2358 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.51 % Allowed : 10.50 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.17), residues: 2130 helix: 1.85 (0.13), residues: 1290 sheet: -0.59 (0.26), residues: 320 loop : -0.54 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 214 HIS 0.007 0.002 HIS A 65 PHE 0.011 0.002 PHE B 202 TYR 0.011 0.002 TYR I 205 ARG 0.003 0.000 ARG B 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 275 time to evaluate : 1.883 Fit side-chains REVERT: A 130 LYS cc_start: 0.8404 (tttm) cc_final: 0.8173 (tttp) REVERT: H 62 ILE cc_start: 0.8305 (pt) cc_final: 0.8052 (pp) REVERT: H 94 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7017 (tp30) REVERT: H 171 ARG cc_start: 0.8542 (mmt-90) cc_final: 0.7999 (mpt90) REVERT: H 174 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7940 (tmtm) REVERT: B 94 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7036 (tp30) REVERT: B 174 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7993 (tmmt) REVERT: B 196 GLU cc_start: 0.7660 (mp0) cc_final: 0.7379 (mm-30) REVERT: C 40 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7866 (mm) REVERT: C 62 ILE cc_start: 0.8312 (pt) cc_final: 0.8058 (pp) REVERT: C 94 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7030 (tp30) REVERT: C 171 ARG cc_start: 0.8532 (mmt-90) cc_final: 0.7994 (mpt90) REVERT: C 174 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7944 (tmtm) REVERT: D 94 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7022 (tp30) REVERT: D 108 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8011 (mp) REVERT: D 174 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7997 (tmmt) REVERT: E 6 ASP cc_start: 0.8263 (t0) cc_final: 0.8025 (t70) REVERT: E 94 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7259 (tp30) REVERT: E 174 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8012 (tmmt) REVERT: F 130 LYS cc_start: 0.8273 (tttm) cc_final: 0.8014 (tttp) REVERT: G 6 ASP cc_start: 0.8269 (t0) cc_final: 0.8032 (t70) REVERT: G 94 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7278 (tp30) REVERT: G 174 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8016 (tmmt) REVERT: I 160 ASN cc_start: 0.7886 (m-40) cc_final: 0.7668 (t0) REVERT: J 94 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7260 (tp30) REVERT: J 130 LYS cc_start: 0.8457 (tttm) cc_final: 0.8247 (tttp) outliers start: 24 outliers final: 6 residues processed: 281 average time/residue: 1.8147 time to fit residues: 551.4465 Evaluate side-chains 294 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 273 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 174 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 174 LYS Chi-restraints excluded: chain J residue 94 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 178 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16770 Z= 0.207 Angle : 0.499 5.318 22920 Z= 0.268 Chirality : 0.046 0.126 2630 Planarity : 0.004 0.032 2950 Dihedral : 10.543 138.110 2358 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 1.64 % Allowed : 10.44 % Favored : 87.92 % 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: 1.45 (0.17), residues: 2130 helix: 1.89 (0.13), residues: 1300 sheet: -0.55 (0.26), residues: 320 loop : -0.32 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 214 HIS 0.005 0.001 HIS A 65 PHE 0.010 0.001 PHE G 191 TYR 0.009 0.001 TYR J 205 ARG 0.002 0.000 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 279 time to evaluate : 2.009 Fit side-chains REVERT: A 94 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7213 (tp30) REVERT: H 62 ILE cc_start: 0.8323 (pt) cc_final: 0.8076 (pp) REVERT: H 94 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6988 (tp30) REVERT: H 171 ARG cc_start: 0.8542 (mmt-90) cc_final: 0.8005 (mpt90) REVERT: H 174 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7950 (tmtm) REVERT: B 94 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7036 (tp30) REVERT: B 108 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8002 (mp) REVERT: B 174 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7994 (tmmt) REVERT: B 196 GLU cc_start: 0.7683 (mp0) cc_final: 0.7374 (mm-30) REVERT: C 62 ILE cc_start: 0.8332 (pt) cc_final: 0.8076 (pp) REVERT: C 94 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6994 (tp30) REVERT: C 171 ARG cc_start: 0.8531 (mmt-90) cc_final: 0.8000 (mpt90) REVERT: C 174 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7954 (tmtm) REVERT: D 94 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7026 (tp30) REVERT: D 108 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8007 (mp) REVERT: D 174 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7996 (tmmt) REVERT: D 196 GLU cc_start: 0.7677 (mp0) cc_final: 0.7405 (mm-30) REVERT: E 6 ASP cc_start: 0.8258 (t0) cc_final: 0.8030 (t70) REVERT: E 94 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7219 (tp30) REVERT: E 174 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8012 (tmmt) REVERT: F 130 LYS cc_start: 0.8285 (tttm) cc_final: 0.8010 (tttp) REVERT: G 6 ASP cc_start: 0.8247 (t0) cc_final: 0.8014 (t70) REVERT: G 94 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7216 (tp30) REVERT: G 174 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8009 (tmmt) REVERT: I 160 ASN cc_start: 0.7881 (m-40) cc_final: 0.7667 (t0) REVERT: J 130 LYS cc_start: 0.8403 (tttm) cc_final: 0.8194 (tttp) outliers start: 26 outliers final: 5 residues processed: 286 average time/residue: 1.7937 time to fit residues: 554.5948 Evaluate side-chains 296 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 276 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 174 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 174 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 166 optimal weight: 0.4980 chunk 17 optimal weight: 0.4980 chunk 128 optimal weight: 0.2980 chunk 102 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16770 Z= 0.147 Angle : 0.455 5.518 22920 Z= 0.240 Chirality : 0.044 0.140 2630 Planarity : 0.004 0.031 2950 Dihedral : 9.827 128.479 2358 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.32 % Allowed : 10.94 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.18), residues: 2130 helix: 2.12 (0.14), residues: 1300 sheet: -0.48 (0.25), residues: 360 loop : -0.27 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 214 HIS 0.003 0.001 HIS A 65 PHE 0.008 0.001 PHE H 191 TYR 0.013 0.001 TYR A 205 ARG 0.001 0.000 ARG B 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 283 time to evaluate : 2.162 Fit side-chains REVERT: A 94 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7097 (tp30) REVERT: A 211 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.8153 (mtm-85) REVERT: H 62 ILE cc_start: 0.8357 (pt) cc_final: 0.8111 (pp) REVERT: H 171 ARG cc_start: 0.8567 (mmt-90) cc_final: 0.8031 (mpt90) REVERT: H 174 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7921 (tmmt) REVERT: B 94 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6962 (tp30) REVERT: B 108 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7930 (mp) REVERT: B 174 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7914 (tmmt) REVERT: B 196 GLU cc_start: 0.7614 (mp0) cc_final: 0.7344 (mm-30) REVERT: C 62 ILE cc_start: 0.8346 (pt) cc_final: 0.8095 (pp) REVERT: C 94 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6887 (tp30) REVERT: C 171 ARG cc_start: 0.8550 (mmt-90) cc_final: 0.8013 (mpt90) REVERT: C 174 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7932 (tmmt) REVERT: D 94 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6956 (tp30) REVERT: D 108 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7958 (mp) REVERT: D 174 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7918 (tmmt) REVERT: D 196 GLU cc_start: 0.7617 (mp0) cc_final: 0.7376 (mm-30) REVERT: E 6 ASP cc_start: 0.8178 (t0) cc_final: 0.7936 (t70) REVERT: E 94 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7074 (tp30) REVERT: E 174 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.7998 (tmmt) REVERT: F 130 LYS cc_start: 0.8253 (tttm) cc_final: 0.8008 (tttp) REVERT: G 94 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7075 (tp30) REVERT: G 174 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8006 (tmmt) REVERT: I 160 ASN cc_start: 0.7879 (m-40) cc_final: 0.7669 (t0) REVERT: J 130 LYS cc_start: 0.8390 (tttm) cc_final: 0.8184 (tttp) outliers start: 21 outliers final: 5 residues processed: 290 average time/residue: 1.7810 time to fit residues: 558.7459 Evaluate side-chains 296 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 277 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 174 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 174 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108233 restraints weight = 16927.968| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 0.82 r_work: 0.3154 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16770 Z= 0.167 Angle : 0.469 5.317 22920 Z= 0.250 Chirality : 0.044 0.124 2630 Planarity : 0.004 0.032 2950 Dihedral : 9.868 128.438 2358 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.32 % Allowed : 11.13 % Favored : 87.55 % 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: 1.69 (0.18), residues: 2130 helix: 2.11 (0.14), residues: 1300 sheet: -0.46 (0.25), residues: 360 loop : -0.30 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 214 HIS 0.003 0.001 HIS A 65 PHE 0.009 0.001 PHE E 191 TYR 0.016 0.001 TYR F 205 ARG 0.001 0.000 ARG D 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8188.07 seconds wall clock time: 144 minutes 11.33 seconds (8651.33 seconds total)