Starting phenix.real_space_refine on Mon Feb 19 19:03:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6m_35200/02_2024/8i6m_35200_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6m_35200/02_2024/8i6m_35200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6m_35200/02_2024/8i6m_35200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6m_35200/02_2024/8i6m_35200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6m_35200/02_2024/8i6m_35200_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6m_35200/02_2024/8i6m_35200_updated.pdb" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.198 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 6 5.21 5 S 108 5.16 5 C 16326 2.51 5 N 4254 2.21 5 O 4764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 112": "OD1" <-> "OD2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A ASP 524": "OD1" <-> "OD2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F GLU 153": "OE1" <-> "OE2" Residue "F PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 309": "OE1" <-> "OE2" Residue "F TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 365": "OE1" <-> "OE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F ASP 524": "OD1" <-> "OD2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D GLU 153": "OE1" <-> "OE2" Residue "D PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 309": "OE1" <-> "OE2" Residue "D TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 365": "OE1" <-> "OE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D ASP 524": "OD1" <-> "OD2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C ASP 524": "OD1" <-> "OD2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B ASP 524": "OD1" <-> "OD2" Residue "E ASP 112": "OD1" <-> "OD2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 309": "OE1" <-> "OE2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 365": "OE1" <-> "OE2" Residue "E GLU 379": "OE1" <-> "OE2" Residue "E ASP 524": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25464 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 12.74, per 1000 atoms: 0.50 Number of scatterers: 25464 At special positions: 0 Unit cell: (169.338, 161.226, 98.358, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 6 15.00 Mg 6 11.99 O 4764 8.00 N 4254 7.00 C 16326 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.72 Conformation dependent library (CDL) restraints added in 4.5 seconds 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 36 sheets defined 31.8% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.27 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.501A pdb=" N LEU A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 57 Processing helix chain 'A' and resid 74 through 86 removed outlier: 3.670A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 118 through 126 Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 189 through 203 removed outlier: 3.929A pdb=" N THR A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 238 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.772A pdb=" N ARG A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 440 through 448 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'F' and resid 15 through 20 removed outlier: 3.500A pdb=" N LEU F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 57 Processing helix chain 'F' and resid 74 through 86 removed outlier: 3.670A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 99 through 109 Processing helix chain 'F' and resid 118 through 126 Proline residue: F 122 - end of helix Processing helix chain 'F' and resid 128 through 130 No H-bonds generated for 'chain 'F' and resid 128 through 130' Processing helix chain 'F' and resid 147 through 153 Processing helix chain 'F' and resid 189 through 203 removed outlier: 3.928A pdb=" N THR F 202 " --> pdb=" O GLY F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 238 Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 251 through 261 Processing helix chain 'F' and resid 270 through 277 Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 301 through 310 removed outlier: 3.772A pdb=" N ARG F 310 " --> pdb=" O SER F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 343 through 348 Processing helix chain 'F' and resid 396 through 401 Processing helix chain 'F' and resid 403 through 405 No H-bonds generated for 'chain 'F' and resid 403 through 405' Processing helix chain 'F' and resid 440 through 448 Processing helix chain 'F' and resid 484 through 493 Processing helix chain 'F' and resid 525 through 532 Processing helix chain 'D' and resid 15 through 20 removed outlier: 3.501A pdb=" N LEU D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 57 Processing helix chain 'D' and resid 74 through 86 removed outlier: 3.671A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 118 through 126 Proline residue: D 122 - end of helix Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 189 through 203 removed outlier: 3.929A pdb=" N THR D 202 " --> pdb=" O GLY D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 238 Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 270 through 277 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 301 through 310 removed outlier: 3.772A pdb=" N ARG D 310 " --> pdb=" O SER D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 343 through 348 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 440 through 448 Processing helix chain 'D' and resid 484 through 493 Processing helix chain 'D' and resid 525 through 532 Processing helix chain 'C' and resid 15 through 20 removed outlier: 3.501A pdb=" N LEU C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 57 Processing helix chain 'C' and resid 74 through 86 removed outlier: 3.670A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 118 through 126 Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 189 through 203 removed outlier: 3.928A pdb=" N THR C 202 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 238 Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 270 through 277 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 301 through 310 removed outlier: 3.772A pdb=" N ARG C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 343 through 348 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 440 through 448 Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 525 through 532 Processing helix chain 'B' and resid 15 through 20 removed outlier: 3.501A pdb=" N LEU B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 57 Processing helix chain 'B' and resid 74 through 86 removed outlier: 3.670A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 118 through 126 Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 189 through 203 removed outlier: 3.928A pdb=" N THR B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 238 Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 270 through 277 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.773A pdb=" N ARG B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 343 through 348 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 440 through 448 Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 525 through 532 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.501A pdb=" N LEU E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 57 Processing helix chain 'E' and resid 74 through 86 removed outlier: 3.670A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 99 through 109 Processing helix chain 'E' and resid 118 through 126 Proline residue: E 122 - end of helix Processing helix chain 'E' and resid 128 through 130 No H-bonds generated for 'chain 'E' and resid 128 through 130' Processing helix chain 'E' and resid 147 through 153 Processing helix chain 'E' and resid 189 through 203 removed outlier: 3.929A pdb=" N THR E 202 " --> pdb=" O GLY E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 238 Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 251 through 261 Processing helix chain 'E' and resid 270 through 277 Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 301 through 310 removed outlier: 3.772A pdb=" N ARG E 310 " --> pdb=" O SER E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 343 through 348 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 403 through 405 No H-bonds generated for 'chain 'E' and resid 403 through 405' Processing helix chain 'E' and resid 440 through 448 Processing helix chain 'E' and resid 484 through 493 Processing helix chain 'E' and resid 525 through 532 Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.473A pdb=" N GLN A 243 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE A 265 " --> pdb=" O MET A 219 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS A 291 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N CYS A 268 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL A 293 " --> pdb=" O CYS A 268 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 89 through 92 removed outlier: 6.333A pdb=" N ILE A 113 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N MET A 69 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 115 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG A 136 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE A 116 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL A 138 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 361 through 363 Processing sheet with id= D, first strand: chain 'A' and resid 509 through 511 removed outlier: 8.311A pdb=" N LYS A 510 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA A 472 " --> pdb=" O LYS A 510 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 455 " --> pdb=" O THR A 475 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 169 through 172 removed outlier: 6.863A pdb=" N PHE A 187 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 411 through 415 removed outlier: 6.736A pdb=" N HIS A 414 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE A 423 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.473A pdb=" N GLN F 243 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE F 265 " --> pdb=" O MET F 219 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS F 291 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N CYS F 268 " --> pdb=" O LYS F 291 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL F 293 " --> pdb=" O CYS F 268 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 89 through 92 removed outlier: 6.333A pdb=" N ILE F 113 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N MET F 69 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU F 115 " --> pdb=" O MET F 69 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG F 136 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE F 116 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL F 138 " --> pdb=" O ILE F 116 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 361 through 363 Processing sheet with id= J, first strand: chain 'F' and resid 509 through 511 removed outlier: 8.311A pdb=" N LYS F 510 " --> pdb=" O PRO F 470 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA F 472 " --> pdb=" O LYS F 510 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU F 455 " --> pdb=" O THR F 475 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 169 through 172 removed outlier: 6.863A pdb=" N PHE F 187 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 411 through 415 removed outlier: 6.735A pdb=" N HIS F 414 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE F 423 " --> pdb=" O HIS F 414 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.473A pdb=" N GLN D 243 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE D 265 " --> pdb=" O MET D 219 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LYS D 291 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N CYS D 268 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL D 293 " --> pdb=" O CYS D 268 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 89 through 92 removed outlier: 6.333A pdb=" N ILE D 113 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N MET D 69 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU D 115 " --> pdb=" O MET D 69 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG D 136 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE D 116 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL D 138 " --> pdb=" O ILE D 116 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 361 through 363 Processing sheet with id= P, first strand: chain 'D' and resid 509 through 511 removed outlier: 8.311A pdb=" N LYS D 510 " --> pdb=" O PRO D 470 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA D 472 " --> pdb=" O LYS D 510 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 455 " --> pdb=" O THR D 475 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 169 through 172 removed outlier: 6.863A pdb=" N PHE D 187 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 411 through 415 removed outlier: 6.736A pdb=" N HIS D 414 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE D 423 " --> pdb=" O HIS D 414 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.473A pdb=" N GLN C 243 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE C 265 " --> pdb=" O MET C 219 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS C 291 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N CYS C 268 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL C 293 " --> pdb=" O CYS C 268 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 89 through 92 removed outlier: 6.333A pdb=" N ILE C 113 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N MET C 69 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU C 115 " --> pdb=" O MET C 69 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG C 136 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE C 116 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL C 138 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 361 through 363 Processing sheet with id= V, first strand: chain 'C' and resid 509 through 511 removed outlier: 8.311A pdb=" N LYS C 510 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA C 472 " --> pdb=" O LYS C 510 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 455 " --> pdb=" O THR C 475 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 169 through 172 removed outlier: 6.863A pdb=" N PHE C 187 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 411 through 415 removed outlier: 6.735A pdb=" N HIS C 414 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE C 423 " --> pdb=" O HIS C 414 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.473A pdb=" N GLN B 243 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE B 265 " --> pdb=" O MET B 219 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS B 291 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N CYS B 268 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL B 293 " --> pdb=" O CYS B 268 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 89 through 92 removed outlier: 6.334A pdb=" N ILE B 113 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N MET B 69 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU B 115 " --> pdb=" O MET B 69 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG B 136 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE B 116 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL B 138 " --> pdb=" O ILE B 116 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 361 through 363 Processing sheet with id= AB, first strand: chain 'B' and resid 509 through 511 removed outlier: 8.312A pdb=" N LYS B 510 " --> pdb=" O PRO B 470 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA B 472 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 455 " --> pdb=" O THR B 475 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 169 through 172 removed outlier: 6.863A pdb=" N PHE B 187 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 411 through 415 removed outlier: 6.737A pdb=" N HIS B 414 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE B 423 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.473A pdb=" N GLN E 243 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE E 265 " --> pdb=" O MET E 219 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LYS E 291 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N CYS E 268 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL E 293 " --> pdb=" O CYS E 268 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 89 through 92 removed outlier: 6.333A pdb=" N ILE E 113 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N MET E 69 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU E 115 " --> pdb=" O MET E 69 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG E 136 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE E 116 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL E 138 " --> pdb=" O ILE E 116 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 361 through 363 Processing sheet with id= AH, first strand: chain 'E' and resid 509 through 511 removed outlier: 8.310A pdb=" N LYS E 510 " --> pdb=" O PRO E 470 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA E 472 " --> pdb=" O LYS E 510 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU E 455 " --> pdb=" O THR E 475 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 169 through 172 removed outlier: 6.864A pdb=" N PHE E 187 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 411 through 415 removed outlier: 6.735A pdb=" N HIS E 414 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE E 423 " --> pdb=" O HIS E 414 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1674 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: 7.85 Time building geometry restraints manager: 10.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4266 1.28 - 1.41: 6288 1.41 - 1.54: 15155 1.54 - 1.68: 127 1.68 - 1.81: 192 Bond restraints: 26028 Sorted by residual: bond pdb=" CA THR F 202 " pdb=" C THR F 202 " ideal model delta sigma weight residual 1.521 1.413 0.107 9.90e-03 1.02e+04 1.17e+02 bond pdb=" CA THR B 202 " pdb=" C THR B 202 " ideal model delta sigma weight residual 1.521 1.414 0.107 9.90e-03 1.02e+04 1.16e+02 bond pdb=" CA THR E 202 " pdb=" C THR E 202 " ideal model delta sigma weight residual 1.521 1.414 0.107 9.90e-03 1.02e+04 1.16e+02 bond pdb=" CA THR A 202 " pdb=" C THR A 202 " ideal model delta sigma weight residual 1.521 1.414 0.106 9.90e-03 1.02e+04 1.16e+02 bond pdb=" CA THR C 202 " pdb=" C THR C 202 " ideal model delta sigma weight residual 1.521 1.414 0.106 9.90e-03 1.02e+04 1.15e+02 ... (remaining 26023 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.85: 639 105.85 - 113.41: 14428 113.41 - 120.97: 12428 120.97 - 128.54: 7533 128.54 - 136.10: 252 Bond angle restraints: 35280 Sorted by residual: angle pdb=" C THR D 202 " pdb=" CA THR D 202 " pdb=" CB THR D 202 " ideal model delta sigma weight residual 110.08 98.28 11.80 1.57e+00 4.06e-01 5.65e+01 angle pdb=" C THR B 202 " pdb=" CA THR B 202 " pdb=" CB THR B 202 " ideal model delta sigma weight residual 110.08 98.30 11.78 1.57e+00 4.06e-01 5.63e+01 angle pdb=" C THR A 202 " pdb=" CA THR A 202 " pdb=" CB THR A 202 " ideal model delta sigma weight residual 110.08 98.30 11.78 1.57e+00 4.06e-01 5.63e+01 angle pdb=" C THR C 202 " pdb=" CA THR C 202 " pdb=" CB THR C 202 " ideal model delta sigma weight residual 110.08 98.32 11.76 1.57e+00 4.06e-01 5.61e+01 angle pdb=" C THR E 202 " pdb=" CA THR E 202 " pdb=" CB THR E 202 " ideal model delta sigma weight residual 110.08 98.32 11.76 1.57e+00 4.06e-01 5.61e+01 ... (remaining 35275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.81: 14725 26.81 - 53.62: 770 53.62 - 80.43: 78 80.43 - 107.24: 30 107.24 - 134.05: 3 Dihedral angle restraints: 15606 sinusoidal: 6378 harmonic: 9228 Sorted by residual: dihedral pdb=" C5' AMP E1002 " pdb=" O5' AMP E1002 " pdb=" P AMP E1002 " pdb=" O3P AMP E1002 " ideal model delta sinusoidal sigma weight residual -60.00 74.06 -134.05 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" C5' AMP A1002 " pdb=" O5' AMP A1002 " pdb=" P AMP A1002 " pdb=" O3P AMP A1002 " ideal model delta sinusoidal sigma weight residual -60.00 74.05 -134.05 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" C5' AMP C1002 " pdb=" O5' AMP C1002 " pdb=" P AMP C1002 " pdb=" O3P AMP C1002 " ideal model delta sinusoidal sigma weight residual -60.00 74.03 -134.03 1 2.00e+01 2.50e-03 4.07e+01 ... (remaining 15603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3818 0.121 - 0.243: 106 0.243 - 0.364: 42 0.364 - 0.486: 12 0.486 - 0.607: 6 Chirality restraints: 3984 Sorted by residual: chirality pdb=" CA MET B 320 " pdb=" N MET B 320 " pdb=" C MET B 320 " pdb=" CB MET B 320 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" CA MET F 320 " pdb=" N MET F 320 " pdb=" C MET F 320 " pdb=" CB MET F 320 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.20e+00 chirality pdb=" CA MET A 320 " pdb=" N MET A 320 " pdb=" C MET A 320 " pdb=" CB MET A 320 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.20e+00 ... (remaining 3981 not shown) Planarity restraints: 4470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA C1001 " -0.232 2.00e-02 2.50e+03 1.79e-01 3.22e+02 pdb=" C11 OLA C1001 " 0.101 2.00e-02 2.50e+03 pdb=" C8 OLA C1001 " -0.101 2.00e-02 2.50e+03 pdb=" C9 OLA C1001 " 0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA D1001 " 0.232 2.00e-02 2.50e+03 1.79e-01 3.22e+02 pdb=" C11 OLA D1001 " -0.101 2.00e-02 2.50e+03 pdb=" C8 OLA D1001 " 0.101 2.00e-02 2.50e+03 pdb=" C9 OLA D1001 " -0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA F1001 " 0.232 2.00e-02 2.50e+03 1.79e-01 3.22e+02 pdb=" C11 OLA F1001 " -0.100 2.00e-02 2.50e+03 pdb=" C8 OLA F1001 " 0.101 2.00e-02 2.50e+03 pdb=" C9 OLA F1001 " -0.233 2.00e-02 2.50e+03 ... (remaining 4467 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 907 2.71 - 3.26: 24864 3.26 - 3.81: 41493 3.81 - 4.35: 56096 4.35 - 4.90: 90642 Nonbonded interactions: 214002 Sorted by model distance: nonbonded pdb=" O1P AMP E1002 " pdb="MG MG E1003 " model vdw 2.165 2.170 nonbonded pdb=" O3P AMP B1002 " pdb="MG MG B1003 " model vdw 2.166 2.170 nonbonded pdb=" O1P AMP C1002 " pdb="MG MG C1003 " model vdw 2.166 2.170 nonbonded pdb=" O1P AMP A1002 " pdb="MG MG A1003 " model vdw 2.166 2.170 nonbonded pdb=" O3P AMP D1002 " pdb="MG MG D1003 " model vdw 2.167 2.170 ... (remaining 213997 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' } 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.380 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 64.330 Find NCS groups from input model: 1.750 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: 0.010 Load rotamer database and sin/cos tables:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 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 : 0.007 0.137 26028 Z= 0.464 Angle : 0.836 11.799 35280 Z= 0.490 Chirality : 0.066 0.607 3984 Planarity : 0.008 0.179 4470 Dihedral : 16.136 134.054 9666 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.17 % Favored : 91.63 % Rotamer: Outliers : 0.80 % Allowed : 18.81 % Favored : 80.39 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 4.35 % 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: -1.29 (0.15), residues: 3156 helix: 0.06 (0.16), residues: 1074 sheet: -1.22 (0.21), residues: 582 loop : -1.31 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 466 HIS 0.005 0.001 HIS E 228 PHE 0.023 0.002 PHE E 186 TYR 0.013 0.001 TYR E 318 ARG 0.001 0.000 ARG A 502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 265 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 MET cc_start: 0.8442 (mtt) cc_final: 0.8103 (mtt) REVERT: D 158 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7951 (mp0) REVERT: D 176 THR cc_start: 0.8097 (t) cc_final: 0.7629 (m) REVERT: D 395 ASN cc_start: 0.8412 (m-40) cc_final: 0.8167 (m110) REVERT: C 58 MET cc_start: 0.8460 (mtt) cc_final: 0.8124 (mtt) REVERT: E 176 THR cc_start: 0.8144 (t) cc_final: 0.7661 (m) REVERT: E 395 ASN cc_start: 0.8389 (m-40) cc_final: 0.8140 (m110) outliers start: 22 outliers final: 4 residues processed: 278 average time/residue: 1.5408 time to fit residues: 489.1368 Evaluate side-chains 214 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 210 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain B residue 163 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 148 optimal weight: 0.5980 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN A 12 GLN A 29 GLN A 117 HIS A 209 GLN A 213 HIS A 226 HIS A 408 HIS A 450 HIS F 6 ASN F 12 GLN F 29 GLN F 117 HIS F 154 GLN F 209 GLN F 213 HIS F 226 HIS F 408 HIS F 450 HIS D 6 ASN D 12 GLN D 29 GLN D 117 HIS D 209 GLN D 213 HIS D 226 HIS D 228 HIS ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 HIS C 6 ASN C 12 GLN C 29 GLN C 117 HIS C 154 GLN C 209 GLN C 213 HIS C 226 HIS C 408 HIS C 450 HIS B 6 ASN B 12 GLN B 29 GLN B 117 HIS B 209 GLN B 213 HIS B 226 HIS B 397 ASN B 408 HIS B 450 HIS E 6 ASN E 12 GLN E 29 GLN E 117 HIS E 209 GLN E 213 HIS E 226 HIS E 228 HIS ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 HIS Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26028 Z= 0.260 Angle : 0.618 7.063 35280 Z= 0.319 Chirality : 0.048 0.194 3984 Planarity : 0.004 0.043 4470 Dihedral : 8.758 108.790 3560 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.56 % Favored : 91.25 % Rotamer: Outliers : 3.34 % Allowed : 16.52 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.26 (0.14), residues: 3156 helix: 0.15 (0.16), residues: 1062 sheet: -0.96 (0.20), residues: 648 loop : -1.47 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 466 HIS 0.009 0.001 HIS D 228 PHE 0.015 0.002 PHE E 225 TYR 0.011 0.002 TYR A 174 ARG 0.002 0.000 ARG F 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 224 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 107 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7379 (t70) REVERT: D 100 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: D 395 ASN cc_start: 0.8506 (m-40) cc_final: 0.8273 (m110) REVERT: C 107 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7402 (t70) REVERT: E 100 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: E 150 ARG cc_start: 0.8043 (mtm110) cc_final: 0.7622 (mpt-90) REVERT: E 395 ASN cc_start: 0.8473 (m-40) cc_final: 0.8230 (m110) outliers start: 92 outliers final: 29 residues processed: 302 average time/residue: 1.3543 time to fit residues: 474.5188 Evaluate side-chains 232 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 199 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 78 optimal weight: 0.0470 chunk 283 optimal weight: 0.0670 chunk 306 optimal weight: 10.0000 chunk 252 optimal weight: 20.0000 chunk 281 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 227 optimal weight: 0.9980 overall best weight: 1.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 GLN F 6 ASN F 449 GLN ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26028 Z= 0.239 Angle : 0.593 6.938 35280 Z= 0.304 Chirality : 0.047 0.191 3984 Planarity : 0.004 0.043 4470 Dihedral : 8.451 92.041 3556 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.35 % Favored : 92.46 % Rotamer: Outliers : 3.52 % Allowed : 16.49 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.15), residues: 3156 helix: 0.14 (0.16), residues: 1062 sheet: -0.69 (0.21), residues: 588 loop : -1.39 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 466 HIS 0.008 0.001 HIS B 228 PHE 0.013 0.002 PHE D 225 TYR 0.011 0.001 TYR D 318 ARG 0.002 0.000 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 208 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7913 (mm-30) REVERT: F 107 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7369 (t70) REVERT: D 100 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: C 107 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7401 (t70) REVERT: C 418 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6573 (pm20) REVERT: C 461 MET cc_start: 0.3863 (OUTLIER) cc_final: 0.3516 (tmt) REVERT: E 100 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: E 150 ARG cc_start: 0.8036 (mtm110) cc_final: 0.7674 (mpt-90) outliers start: 97 outliers final: 29 residues processed: 289 average time/residue: 1.3626 time to fit residues: 455.3656 Evaluate side-chains 235 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 199 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 147 optimal weight: 0.0050 chunk 31 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 284 optimal weight: 0.9990 chunk 301 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 269 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN D 408 HIS E 408 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26028 Z= 0.207 Angle : 0.582 7.533 35280 Z= 0.297 Chirality : 0.046 0.176 3984 Planarity : 0.004 0.042 4470 Dihedral : 8.078 66.679 3556 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.19 % Favored : 92.62 % Rotamer: Outliers : 3.12 % Allowed : 17.21 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.01 (0.15), residues: 3156 helix: 0.21 (0.16), residues: 1068 sheet: -0.57 (0.21), residues: 588 loop : -1.31 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 466 HIS 0.007 0.001 HIS A 228 PHE 0.012 0.001 PHE D 225 TYR 0.011 0.001 TYR C 318 ARG 0.001 0.000 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 218 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 107 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7372 (t70) REVERT: C 107 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7385 (t70) REVERT: C 343 GLN cc_start: 0.7460 (mp10) cc_final: 0.6754 (mt0) REVERT: C 365 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: C 461 MET cc_start: 0.3824 (OUTLIER) cc_final: 0.3459 (tmt) REVERT: E 150 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7671 (mpt-90) REVERT: E 428 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7826 (mmtt) outliers start: 86 outliers final: 37 residues processed: 283 average time/residue: 1.3182 time to fit residues: 435.0868 Evaluate side-chains 248 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 206 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.0000 chunk 171 optimal weight: 0.0670 chunk 4 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 124 optimal weight: 0.0980 chunk 257 optimal weight: 0.7980 chunk 208 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 270 optimal weight: 5.9990 chunk 76 optimal weight: 0.1980 overall best weight: 0.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 331 GLN D 449 GLN ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26028 Z= 0.131 Angle : 0.530 7.237 35280 Z= 0.265 Chirality : 0.044 0.133 3984 Planarity : 0.003 0.036 4470 Dihedral : 7.485 59.631 3556 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.69 % Favored : 93.12 % Rotamer: Outliers : 2.65 % Allowed : 18.05 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.73 (0.15), residues: 3156 helix: 0.41 (0.16), residues: 1068 sheet: -0.39 (0.22), residues: 582 loop : -1.14 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 466 HIS 0.005 0.001 HIS C 267 PHE 0.009 0.001 PHE D 225 TYR 0.009 0.001 TYR A 148 ARG 0.001 0.000 ARG E 502 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 232 time to evaluate : 3.042 Fit side-chains revert: symmetry clash REVERT: F 107 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7486 (t70) REVERT: F 365 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: C 107 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7515 (t70) REVERT: C 365 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: B 418 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6865 (pt0) REVERT: E 150 ARG cc_start: 0.7990 (mtm110) cc_final: 0.7651 (mpt-90) REVERT: E 395 ASN cc_start: 0.8498 (m-40) cc_final: 0.8205 (m-40) outliers start: 73 outliers final: 32 residues processed: 285 average time/residue: 1.2981 time to fit residues: 430.5152 Evaluate side-chains 242 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 205 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 9.9990 chunk 271 optimal weight: 0.0870 chunk 59 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 301 optimal weight: 8.9990 chunk 250 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS A 331 GLN D 395 ASN C 331 GLN B 228 HIS ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26028 Z= 0.201 Angle : 0.569 7.894 35280 Z= 0.289 Chirality : 0.046 0.169 3984 Planarity : 0.004 0.040 4470 Dihedral : 7.608 59.839 3556 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.81 % Favored : 93.00 % Rotamer: Outliers : 2.29 % Allowed : 19.28 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.72 (0.15), residues: 3156 helix: 0.49 (0.16), residues: 1086 sheet: -0.37 (0.22), residues: 588 loop : -1.22 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 466 HIS 0.013 0.001 HIS A 228 PHE 0.013 0.001 PHE E 225 TYR 0.011 0.001 TYR E 318 ARG 0.001 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 209 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 107 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7351 (t70) REVERT: F 365 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: D 150 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7629 (mpt-90) REVERT: C 107 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7374 (t70) REVERT: C 343 GLN cc_start: 0.7362 (mp10) cc_final: 0.6650 (mt0) REVERT: C 365 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: E 150 ARG cc_start: 0.8008 (mtm110) cc_final: 0.7668 (mpt-90) outliers start: 63 outliers final: 30 residues processed: 256 average time/residue: 1.3230 time to fit residues: 394.3084 Evaluate side-chains 239 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 205 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 171 optimal weight: 0.1980 chunk 220 optimal weight: 5.9990 chunk 170 optimal weight: 0.6980 chunk 254 optimal weight: 20.0000 chunk 168 optimal weight: 1.9990 chunk 300 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26028 Z= 0.184 Angle : 0.564 6.513 35280 Z= 0.285 Chirality : 0.045 0.165 3984 Planarity : 0.004 0.040 4470 Dihedral : 7.541 59.986 3556 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.91 % Favored : 92.90 % Rotamer: Outliers : 2.00 % Allowed : 19.54 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.73 (0.15), residues: 3156 helix: 0.48 (0.16), residues: 1062 sheet: -0.38 (0.22), residues: 576 loop : -1.19 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 466 HIS 0.006 0.001 HIS F 228 PHE 0.012 0.001 PHE D 225 TYR 0.010 0.001 TYR B 318 ARG 0.001 0.000 ARG F 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 203 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 107 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7351 (t70) REVERT: F 365 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: D 150 ARG cc_start: 0.8010 (mtm110) cc_final: 0.7650 (mpt-90) REVERT: D 505 LEU cc_start: 0.3643 (OUTLIER) cc_final: 0.3270 (mt) REVERT: C 107 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7376 (t70) REVERT: C 365 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: E 150 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7683 (mpt-90) REVERT: E 154 GLN cc_start: 0.7252 (mm-40) cc_final: 0.7005 (pp30) outliers start: 55 outliers final: 38 residues processed: 251 average time/residue: 1.3395 time to fit residues: 391.3194 Evaluate side-chains 245 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 202 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 4.9990 chunk 120 optimal weight: 0.4980 chunk 179 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 204 optimal weight: 30.0000 chunk 148 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 236 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN A 397 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26028 Z= 0.192 Angle : 0.570 6.834 35280 Z= 0.289 Chirality : 0.046 0.165 3984 Planarity : 0.004 0.040 4470 Dihedral : 7.512 59.983 3556 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.91 % Favored : 92.90 % Rotamer: Outliers : 2.29 % Allowed : 19.61 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.74 (0.15), residues: 3156 helix: 0.46 (0.16), residues: 1062 sheet: -0.42 (0.22), residues: 576 loop : -1.18 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 466 HIS 0.006 0.001 HIS C 228 PHE 0.013 0.001 PHE E 225 TYR 0.012 0.001 TYR F 318 ARG 0.001 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 210 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 107 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7361 (t70) REVERT: D 150 ARG cc_start: 0.8008 (mtm110) cc_final: 0.7652 (mpt-90) REVERT: D 505 LEU cc_start: 0.3528 (OUTLIER) cc_final: 0.3154 (mt) REVERT: C 107 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7381 (t70) REVERT: C 365 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: E 150 ARG cc_start: 0.8008 (mtm110) cc_final: 0.7682 (mpt-90) REVERT: E 154 GLN cc_start: 0.7255 (mm-40) cc_final: 0.7008 (pp30) outliers start: 63 outliers final: 44 residues processed: 263 average time/residue: 1.3344 time to fit residues: 408.8615 Evaluate side-chains 253 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 205 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 5.9990 chunk 288 optimal weight: 0.0980 chunk 262 optimal weight: 5.9990 chunk 280 optimal weight: 0.0040 chunk 168 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 253 optimal weight: 0.4980 chunk 265 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN C 331 GLN E 331 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26028 Z= 0.168 Angle : 0.557 7.196 35280 Z= 0.281 Chirality : 0.045 0.159 3984 Planarity : 0.004 0.039 4470 Dihedral : 7.330 60.328 3556 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.78 % Favored : 93.03 % Rotamer: Outliers : 2.07 % Allowed : 19.93 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.69 (0.15), residues: 3156 helix: 0.52 (0.17), residues: 1062 sheet: -0.46 (0.22), residues: 582 loop : -1.12 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 466 HIS 0.006 0.001 HIS E 228 PHE 0.012 0.001 PHE D 225 TYR 0.010 0.001 TYR A 234 ARG 0.001 0.000 ARG D 502 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 206 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 107 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7354 (t70) REVERT: F 365 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: D 150 ARG cc_start: 0.8018 (mtm110) cc_final: 0.7672 (mpt-90) REVERT: D 505 LEU cc_start: 0.3517 (OUTLIER) cc_final: 0.3138 (mt) REVERT: C 107 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7549 (t70) REVERT: C 365 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: E 150 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7677 (mpt-90) REVERT: E 154 GLN cc_start: 0.7254 (mm-40) cc_final: 0.7009 (pp30) REVERT: E 395 ASN cc_start: 0.8604 (m-40) cc_final: 0.8380 (m-40) outliers start: 57 outliers final: 40 residues processed: 256 average time/residue: 1.2928 time to fit residues: 386.9668 Evaluate side-chains 246 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 201 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.7980 chunk 296 optimal weight: 0.0370 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 0.0030 chunk 205 optimal weight: 6.9990 chunk 310 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 chunk 247 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 overall best weight: 0.9070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26028 Z= 0.190 Angle : 0.572 7.334 35280 Z= 0.290 Chirality : 0.046 0.165 3984 Planarity : 0.004 0.040 4470 Dihedral : 7.368 63.169 3556 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.07 % Favored : 92.74 % Rotamer: Outliers : 1.78 % Allowed : 20.33 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.79 (0.15), residues: 3156 helix: 0.49 (0.16), residues: 1062 sheet: -0.64 (0.21), residues: 636 loop : -1.18 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 466 HIS 0.006 0.001 HIS C 228 PHE 0.013 0.001 PHE E 225 TYR 0.012 0.001 TYR D 318 ARG 0.002 0.000 ARG E 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 204 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 107 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7361 (t70) REVERT: F 365 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: D 150 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7660 (mpt-90) REVERT: D 505 LEU cc_start: 0.3493 (OUTLIER) cc_final: 0.3142 (mt) REVERT: C 107 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7379 (t70) REVERT: E 150 ARG cc_start: 0.8002 (mtm110) cc_final: 0.7682 (mpt-90) REVERT: E 154 GLN cc_start: 0.7251 (mm-40) cc_final: 0.7002 (pp30) REVERT: E 395 ASN cc_start: 0.8614 (m-40) cc_final: 0.8393 (m-40) outliers start: 49 outliers final: 42 residues processed: 245 average time/residue: 1.3014 time to fit residues: 373.9887 Evaluate side-chains 250 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 204 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 365 GLU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.6980 chunk 263 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 228 optimal weight: 0.0980 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 247 optimal weight: 0.6980 chunk 103 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.168436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123924 restraints weight = 28553.376| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.93 r_work: 0.3208 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26028 Z= 0.163 Angle : 0.553 7.931 35280 Z= 0.279 Chirality : 0.045 0.155 3984 Planarity : 0.004 0.039 4470 Dihedral : 7.199 63.635 3556 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.81 % Favored : 93.00 % Rotamer: Outliers : 1.89 % Allowed : 20.30 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.64 (0.15), residues: 3156 helix: 0.54 (0.17), residues: 1062 sheet: -0.44 (0.22), residues: 582 loop : -1.07 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 230 HIS 0.006 0.001 HIS D 228 PHE 0.011 0.001 PHE E 225 TYR 0.008 0.001 TYR A 148 ARG 0.001 0.000 ARG D 502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8092.47 seconds wall clock time: 145 minutes 28.18 seconds (8728.18 seconds total)