Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 15:21:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/07_2023/8bc3_15961_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/07_2023/8bc3_15961.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/07_2023/8bc3_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_15961/07_2023/8bc3_15961_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/07_2023/8bc3_15961_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/07_2023/8bc3_15961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/07_2023/8bc3_15961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/07_2023/8bc3_15961_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bc3_15961/07_2023/8bc3_15961_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 9.44, per 1000 atoms: 0.56 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: 7.20 Conformation dependent library (CDL) restraints added in 2.3 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: 1.41 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: 5.04 Time building geometry restraints manager: 7.62 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 - 17.25: 8380 17.25 - 34.50: 808 34.50 - 51.76: 332 51.76 - 69.01: 80 69.01 - 86.26: 40 Dihedral angle restraints: 9640 sinusoidal: 3320 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 9637 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: 2.310 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: 9.150 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 44.840 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 71.600 ------------------------------------------------------------------------------- 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 : 17.988 86.259 5560 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 % 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 *********************** 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 : 1.848 Fit side-chains outliers start: 190 outliers final: 9 residues processed: 530 average time/residue: 1.3373 time to fit residues: 782.9915 Evaluate side-chains 300 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 291 time to evaluate : 1.868 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 2.3821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 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: 0.9990 chunk 122 optimal weight: 0.6980 chunk 190 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 150 GLN A 172 ASN A 175 GLN A 200 HIS H 63 ASN H 85 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 172 ASN B 175 GLN B 200 HIS B 216 ASN C 63 ASN C 85 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 172 ASN D 175 GLN D 200 HIS D 216 ASN E 31 HIS 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: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2487 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= 0.196 Angle : 0.543 5.509 22920 Z= 0.288 Chirality : 0.045 0.142 2630 Planarity : 0.006 0.075 2950 Dihedral : 5.476 55.323 2310 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 1.70 % 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: -0.51 (0.17), residues: 2130 helix: 0.40 (0.13), residues: 1300 sheet: -1.29 (0.26), residues: 300 loop : -1.32 (0.24), residues: 530 *********************** 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: 27 poor density : 280 time to evaluate : 2.087 Fit side-chains outliers start: 27 outliers final: 10 residues processed: 294 average time/residue: 1.7287 time to fit residues: 552.2378 Evaluate side-chains 280 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 270 time to evaluate : 2.027 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 2.2812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 129 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 191 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 153 optimal weight: 0.8980 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 85 ASN A 150 GLN H 150 GLN B 85 ASN B 150 GLN 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 Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2890 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= 0.163 Angle : 0.482 5.253 22920 Z= 0.254 Chirality : 0.044 0.127 2630 Planarity : 0.005 0.047 2950 Dihedral : 5.152 53.802 2310 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 1.32 % 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: 0.82 (0.17), residues: 2130 helix: 1.45 (0.13), residues: 1310 sheet: -0.75 (0.27), residues: 300 loop : -0.84 (0.25), residues: 520 *********************** 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 304 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 283 time to evaluate : 1.854 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 296 average time/residue: 1.7449 time to fit residues: 560.2004 Evaluate side-chains 278 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 267 time to evaluate : 1.927 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 3 average time/residue: 0.2684 time to fit residues: 3.7378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 181 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 111 ASN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 16770 Z= 0.236 Angle : 0.540 5.283 22920 Z= 0.289 Chirality : 0.047 0.132 2630 Planarity : 0.005 0.046 2950 Dihedral : 5.254 51.115 2310 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2130 helix: 1.65 (0.13), residues: 1290 sheet: -0.73 (0.26), residues: 320 loop : -0.61 (0.27), residues: 520 *********************** 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 300 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 274 time to evaluate : 1.979 Fit side-chains outliers start: 26 outliers final: 9 residues processed: 284 average time/residue: 1.7838 time to fit residues: 549.2634 Evaluate side-chains 269 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 260 time to evaluate : 1.883 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 1.6783 time to fit residues: 4.2058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 151 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 173 optimal weight: 0.0470 chunk 140 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.0086 ------------------------------------------------------------------------------- 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 111 ASN D 150 GLN E 150 GLN G 150 GLN J 150 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3116 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= 0.189 Angle : 0.494 5.314 22920 Z= 0.262 Chirality : 0.045 0.126 2630 Planarity : 0.004 0.033 2950 Dihedral : 5.087 49.432 2310 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer Outliers : 1.13 % 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: 1.36 (0.18), residues: 2130 helix: 1.84 (0.14), residues: 1290 sheet: -0.64 (0.26), residues: 320 loop : -0.34 (0.27), residues: 520 *********************** 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 288 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 270 time to evaluate : 1.769 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 281 average time/residue: 1.7587 time to fit residues: 535.5881 Evaluate side-chains 278 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 270 time to evaluate : 1.837 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.3761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 40 optimal weight: 0.3980 chunk 119 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 31 HIS B 150 GLN C 150 GLN D 31 HIS 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 16770 Z= 0.358 Angle : 0.634 6.704 22920 Z= 0.340 Chirality : 0.052 0.183 2630 Planarity : 0.005 0.050 2950 Dihedral : 5.581 51.052 2310 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2130 helix: 1.48 (0.13), residues: 1290 sheet: -0.63 (0.25), residues: 320 loop : -0.68 (0.27), residues: 520 *********************** 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 295 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 269 time to evaluate : 1.975 Fit side-chains outliers start: 26 outliers final: 9 residues processed: 276 average time/residue: 1.8412 time to fit residues: 550.5855 Evaluate side-chains 272 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 263 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 3 average time/residue: 0.7396 time to fit residues: 5.0718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 202 optimal weight: 0.5980 chunk 126 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 0.8336 moved from start: 0.3200 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 : 0.480 5.354 22920 Z= 0.254 Chirality : 0.044 0.125 2630 Planarity : 0.004 0.032 2950 Dihedral : 5.068 49.929 2310 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.18), residues: 2130 helix: 1.87 (0.13), residues: 1300 sheet: -0.52 (0.24), residues: 360 loop : -0.39 (0.29), residues: 470 *********************** 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 293 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 278 time to evaluate : 1.937 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 286 average time/residue: 1.8099 time to fit residues: 559.8398 Evaluate side-chains 280 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 272 time to evaluate : 1.887 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 2 average time/residue: 0.2801 time to fit residues: 3.2162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 120 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 184 optimal weight: 0.0970 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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** F 150 GLN ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 16770 Z= 0.237 Angle : 0.533 5.354 22920 Z= 0.285 Chirality : 0.047 0.127 2630 Planarity : 0.004 0.032 2950 Dihedral : 5.302 51.442 2310 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer Outliers : 0.82 % 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: 1.36 (0.17), residues: 2130 helix: 1.81 (0.13), residues: 1300 sheet: -0.54 (0.26), residues: 320 loop : -0.36 (0.27), residues: 510 *********************** 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 285 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 272 time to evaluate : 1.997 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 278 average time/residue: 1.8063 time to fit residues: 544.1277 Evaluate side-chains 274 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 268 time to evaluate : 1.966 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 2.4400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 178 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8339 moved from start: 0.3225 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= 0.180 Angle : 0.487 5.350 22920 Z= 0.258 Chirality : 0.045 0.126 2630 Planarity : 0.004 0.032 2950 Dihedral : 5.131 52.817 2310 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.18), residues: 2130 helix: 2.02 (0.14), residues: 1290 sheet: -0.65 (0.24), residues: 380 loop : -0.33 (0.29), residues: 460 *********************** 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 285 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 271 time to evaluate : 1.876 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 277 average time/residue: 1.9052 time to fit residues: 570.3505 Evaluate side-chains 275 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 267 time to evaluate : 1.932 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 2 average time/residue: 0.3086 time to fit residues: 3.3967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 94 optimal weight: 0.0980 chunk 138 optimal weight: 0.5980 chunk 209 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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: 0.8327 moved from start: 0.3228 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= 0.156 Angle : 0.464 5.334 22920 Z= 0.246 Chirality : 0.044 0.123 2630 Planarity : 0.004 0.031 2950 Dihedral : 5.016 55.629 2310 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer Outliers : 0.57 % 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: 2.11 (0.14), residues: 1300 sheet: -0.46 (0.25), residues: 360 loop : -0.27 (0.28), residues: 470 ********************** 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 282 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 273 time to evaluate : 1.891 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 279 average time/residue: 1.8301 time to fit residues: 552.2358 Evaluate side-chains 280 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 272 time to evaluate : 2.052 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 2 average time/residue: 0.3066 time to fit residues: 3.5547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 24 optimal weight: 0.0270 chunk 46 optimal weight: 0.6980 chunk 166 optimal weight: 0.0770 chunk 69 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.121527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110144 restraints weight = 17038.926| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 0.82 r_work: 0.3182 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3268 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= 0.137 Angle : 0.438 5.333 22920 Z= 0.232 Chirality : 0.043 0.121 2630 Planarity : 0.004 0.030 2950 Dihedral : 4.912 57.713 2310 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.18), residues: 2130 helix: 2.21 (0.14), residues: 1300 sheet: -0.40 (0.25), residues: 360 loop : -0.12 (0.28), residues: 470 =============================================================================== Job complete usr+sys time: 7909.66 seconds wall clock time: 140 minutes 1.45 seconds (8401.45 seconds total)