Starting phenix.real_space_refine on Mon Feb 19 18:53:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i51_35190/02_2024/8i51_35190_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i51_35190/02_2024/8i51_35190.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i51_35190/02_2024/8i51_35190_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i51_35190/02_2024/8i51_35190_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i51_35190/02_2024/8i51_35190_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i51_35190/02_2024/8i51_35190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i51_35190/02_2024/8i51_35190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i51_35190/02_2024/8i51_35190_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i51_35190/02_2024/8i51_35190_neut_updated.pdb" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.141 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 16266 2.51 5 N 4254 2.21 5 O 4776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A ASP 445": "OD1" <-> "OD2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A ASP 524": "OD1" <-> "OD2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ASP 342": "OD1" <-> "OD2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B ASP 425": "OD1" <-> "OD2" Residue "B ASP 445": "OD1" <-> "OD2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B ASP 524": "OD1" <-> "OD2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 143": "OD1" <-> "OD2" Residue "C TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ASP 342": "OD1" <-> "OD2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C ASP 425": "OD1" <-> "OD2" Residue "C ASP 445": "OD1" <-> "OD2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "C ASP 524": "OD1" <-> "OD2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "D TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ASP 342": "OD1" <-> "OD2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D GLU 365": "OE1" <-> "OE2" Residue "D ASP 425": "OD1" <-> "OD2" Residue "D ASP 445": "OD1" <-> "OD2" Residue "D GLU 503": "OE1" <-> "OE2" Residue "D ASP 524": "OD1" <-> "OD2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "E TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 112": "OD1" <-> "OD2" Residue "E TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 143": "OD1" <-> "OD2" Residue "E TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E ASP 342": "OD1" <-> "OD2" Residue "E GLU 346": "OE1" <-> "OE2" Residue "E GLU 365": "OE1" <-> "OE2" Residue "E ASP 425": "OD1" <-> "OD2" Residue "E ASP 445": "OD1" <-> "OD2" Residue "E GLU 503": "OE1" <-> "OE2" Residue "E ASP 524": "OD1" <-> "OD2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "F TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 143": "OD1" <-> "OD2" Residue "F TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F ASP 342": "OD1" <-> "OD2" Residue "F GLU 346": "OE1" <-> "OE2" Residue "F GLU 365": "OE1" <-> "OE2" Residue "F ASP 425": "OD1" <-> "OD2" Residue "F ASP 445": "OD1" <-> "OD2" Residue "F GLU 503": "OE1" <-> "OE2" Residue "F ASP 524": "OD1" <-> "OD2" Residue "F GLU 527": "OE1" <-> "OE2" 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: 25416 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: "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: "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: "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: "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: "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: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'OP3': 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: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'OP3': 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: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'OP3': 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: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'OP3': 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: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'OP3': 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: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'OP3': 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: {'OP3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 13.44, per 1000 atoms: 0.53 Number of scatterers: 25416 At special positions: 0 Unit cell: (169.338, 158.184, 94.302, 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 4776 8.00 N 4254 7.00 C 16266 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: 9.85 Conformation dependent library (CDL) restraints added in 4.6 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: 114 helices and 42 sheets defined 30.9% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.33 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.540A pdb=" N LEU A 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE A 20 " --> pdb=" O ASN A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 57 Processing helix chain 'A' and resid 74 through 86 removed outlier: 3.664A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.686A 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 152 Processing helix chain 'A' and resid 189 through 203 removed outlier: 3.525A pdb=" N THR A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 238 Proline residue: A 233 - end of helix removed outlier: 3.665A pdb=" N ALA A 236 " --> pdb=" O PRO A 233 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A 237 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.545A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.650A pdb=" N ARG A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' 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 446 Processing helix chain 'A' and resid 484 through 493 removed outlier: 3.622A pdb=" N ALA A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.524A pdb=" N LYS A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 20 removed outlier: 3.540A pdb=" N LEU B 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE B 20 " --> pdb=" O ASN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 57 Processing helix chain 'B' and resid 74 through 86 removed outlier: 3.664A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.686A 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 152 Processing helix chain 'B' and resid 189 through 203 removed outlier: 3.525A pdb=" N THR B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 238 Proline residue: B 233 - end of helix removed outlier: 3.666A pdb=" N ALA B 236 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 237 " --> pdb=" O TYR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 261 removed outlier: 3.545A pdb=" N ASN B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.650A pdb=" N ARG B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' 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 446 Processing helix chain 'B' and resid 484 through 493 removed outlier: 3.622A pdb=" N ALA B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP B 493 " --> pdb=" O GLY B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 531 removed outlier: 3.524A pdb=" N LYS B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 20 removed outlier: 3.539A pdb=" N LEU C 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE C 20 " --> pdb=" O ASN C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 57 Processing helix chain 'C' and resid 74 through 86 removed outlier: 3.664A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.686A 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 152 Processing helix chain 'C' and resid 189 through 203 removed outlier: 3.525A pdb=" N THR C 202 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 238 Proline residue: C 233 - end of helix removed outlier: 3.665A pdb=" N ALA C 236 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR C 237 " --> pdb=" O TYR C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 261 removed outlier: 3.545A pdb=" N ASN C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 301 through 310 removed outlier: 3.651A pdb=" N ARG C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' 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 446 Processing helix chain 'C' and resid 484 through 493 removed outlier: 3.623A pdb=" N ALA C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 493 " --> pdb=" O GLY C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 531 removed outlier: 3.525A pdb=" N LYS C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 20 removed outlier: 3.540A pdb=" N LEU D 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE D 20 " --> pdb=" O ASN D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 57 Processing helix chain 'D' and resid 74 through 86 removed outlier: 3.663A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.686A 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 152 Processing helix chain 'D' and resid 189 through 203 removed outlier: 3.525A pdb=" N THR D 202 " --> pdb=" O GLY D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 238 Proline residue: D 233 - end of helix removed outlier: 3.665A pdb=" N ALA D 236 " --> pdb=" O PRO D 233 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR D 237 " --> pdb=" O TYR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 261 removed outlier: 3.545A pdb=" N ASN D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 278 Processing helix chain 'D' and resid 301 through 310 removed outlier: 3.650A pdb=" N ARG D 310 " --> pdb=" O SER D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' 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 446 Processing helix chain 'D' and resid 484 through 493 removed outlier: 3.623A pdb=" N ALA D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP D 493 " --> pdb=" O GLY D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 531 removed outlier: 3.524A pdb=" N LYS D 530 " --> pdb=" O LYS D 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.541A pdb=" N LEU E 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE E 20 " --> pdb=" O ASN E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 57 Processing helix chain 'E' and resid 74 through 86 removed outlier: 3.663A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.686A 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 152 Processing helix chain 'E' and resid 189 through 203 removed outlier: 3.524A pdb=" N THR E 202 " --> pdb=" O GLY E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 238 Proline residue: E 233 - end of helix removed outlier: 3.665A pdb=" N ALA E 236 " --> pdb=" O PRO E 233 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR E 237 " --> pdb=" O TYR E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 261 removed outlier: 3.545A pdb=" N ASN E 256 " --> pdb=" O ASP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 278 Processing helix chain 'E' and resid 301 through 310 removed outlier: 3.650A pdb=" N ARG E 310 " --> pdb=" O SER E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' 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 446 Processing helix chain 'E' and resid 484 through 493 removed outlier: 3.622A pdb=" N ALA E 491 " --> pdb=" O LEU E 487 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP E 493 " --> pdb=" O GLY E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 531 removed outlier: 3.524A pdb=" N LYS E 530 " --> pdb=" O LYS E 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 20 removed outlier: 3.540A pdb=" N LEU F 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE F 20 " --> pdb=" O ASN F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 57 Processing helix chain 'F' and resid 74 through 86 removed outlier: 3.663A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.686A 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 152 Processing helix chain 'F' and resid 189 through 203 removed outlier: 3.525A pdb=" N THR F 202 " --> pdb=" O GLY F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 238 Proline residue: F 233 - end of helix removed outlier: 3.665A pdb=" N ALA F 236 " --> pdb=" O PRO F 233 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR F 237 " --> pdb=" O TYR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 261 removed outlier: 3.546A pdb=" N ASN F 256 " --> pdb=" O ASP F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 278 Processing helix chain 'F' and resid 301 through 310 removed outlier: 3.651A pdb=" N ARG F 310 " --> pdb=" O SER F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' 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 446 Processing helix chain 'F' and resid 484 through 493 removed outlier: 3.622A pdb=" N ALA F 491 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP F 493 " --> pdb=" O GLY F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 531 removed outlier: 3.524A pdb=" N LYS F 530 " --> pdb=" O LYS F 526 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.436A pdb=" N GLN A 243 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE A 265 " --> pdb=" O MET A 219 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS A 268 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 89 through 92 removed outlier: 6.415A pdb=" N ILE A 113 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N MET A 69 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 115 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG A 136 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE A 116 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.949A 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: 8.745A pdb=" N LYS A 510 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA A 472 " --> pdb=" O LYS A 510 " (cutoff:3.500A) removed outlier: 3.817A 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: 6.877A pdb=" N PHE A 187 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 317 through 319 Processing sheet with id= G, first strand: chain 'A' and resid 411 through 415 removed outlier: 6.672A pdb=" N HIS A 414 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE A 423 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.436A pdb=" N GLN B 243 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE B 265 " --> pdb=" O MET B 219 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS B 268 " --> pdb=" O VAL B 293 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 89 through 92 removed outlier: 6.415A pdb=" N ILE B 113 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N MET B 69 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 115 " --> pdb=" O MET B 69 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG B 136 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE B 116 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL B 138 " --> pdb=" O ILE B 116 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 361 through 363 Processing sheet with id= K, first strand: chain 'B' and resid 509 through 511 removed outlier: 8.745A pdb=" N LYS B 510 " --> pdb=" O PRO B 470 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA B 472 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 455 " --> pdb=" O THR B 475 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 169 through 172 removed outlier: 6.877A pdb=" N PHE B 187 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 317 through 319 Processing sheet with id= N, first strand: chain 'B' and resid 411 through 415 removed outlier: 6.672A pdb=" N HIS B 414 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE B 423 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.437A pdb=" N GLN C 243 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE C 265 " --> pdb=" O MET C 219 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS C 268 " --> pdb=" O VAL C 293 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 89 through 92 removed outlier: 6.416A pdb=" N ILE C 113 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N MET C 69 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU C 115 " --> pdb=" O MET C 69 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG C 136 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE C 116 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL C 138 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 361 through 363 Processing sheet with id= R, first strand: chain 'C' and resid 509 through 511 removed outlier: 8.745A pdb=" N LYS C 510 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA C 472 " --> pdb=" O LYS C 510 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU C 455 " --> pdb=" O THR C 475 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 169 through 172 removed outlier: 6.878A pdb=" N PHE C 187 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 317 through 319 Processing sheet with id= U, first strand: chain 'C' and resid 411 through 415 removed outlier: 6.672A pdb=" N HIS C 414 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE C 423 " --> pdb=" O HIS C 414 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.437A pdb=" N GLN D 243 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE D 265 " --> pdb=" O MET D 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS D 268 " --> pdb=" O VAL D 293 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 89 through 92 removed outlier: 6.416A pdb=" N ILE D 113 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N MET D 69 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU D 115 " --> pdb=" O MET D 69 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG D 136 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE D 116 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL D 138 " --> pdb=" O ILE D 116 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 361 through 363 Processing sheet with id= Y, first strand: chain 'D' and resid 509 through 511 removed outlier: 8.744A pdb=" N LYS D 510 " --> pdb=" O PRO D 470 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA D 472 " --> pdb=" O LYS D 510 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU D 455 " --> pdb=" O THR D 475 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 169 through 172 removed outlier: 6.877A pdb=" N PHE D 187 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 317 through 319 Processing sheet with id= AB, first strand: chain 'D' and resid 411 through 415 removed outlier: 6.672A pdb=" N HIS D 414 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE D 423 " --> pdb=" O HIS D 414 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.436A pdb=" N GLN E 243 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE E 265 " --> pdb=" O MET E 219 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS E 268 " --> pdb=" O VAL E 293 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 89 through 92 removed outlier: 6.415A pdb=" N ILE E 113 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N MET E 69 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU E 115 " --> pdb=" O MET E 69 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG E 136 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE E 116 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL E 138 " --> pdb=" O ILE E 116 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 361 through 363 Processing sheet with id= AF, first strand: chain 'E' and resid 509 through 511 removed outlier: 8.745A pdb=" N LYS E 510 " --> pdb=" O PRO E 470 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA E 472 " --> pdb=" O LYS E 510 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU E 455 " --> pdb=" O THR E 475 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 169 through 172 removed outlier: 6.878A pdb=" N PHE E 187 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 317 through 319 Processing sheet with id= AI, first strand: chain 'E' and resid 411 through 415 removed outlier: 6.672A pdb=" N HIS E 414 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE E 423 " --> pdb=" O HIS E 414 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.437A pdb=" N GLN F 243 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE F 265 " --> pdb=" O MET F 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS F 268 " --> pdb=" O VAL F 293 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 89 through 92 removed outlier: 6.416A pdb=" N ILE F 113 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N MET F 69 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU F 115 " --> pdb=" O MET F 69 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG F 136 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE F 116 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL F 138 " --> pdb=" O ILE F 116 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 361 through 363 Processing sheet with id= AM, first strand: chain 'F' and resid 509 through 511 removed outlier: 8.745A pdb=" N LYS F 510 " --> pdb=" O PRO F 470 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA F 472 " --> pdb=" O LYS F 510 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU F 455 " --> pdb=" O THR F 475 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 169 through 172 removed outlier: 6.877A pdb=" N PHE F 187 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 317 through 319 Processing sheet with id= AP, first strand: chain 'F' and resid 411 through 415 removed outlier: 6.672A pdb=" N HIS F 414 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE F 423 " --> pdb=" O HIS F 414 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1602 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: 8.66 Time building geometry restraints manager: 10.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4266 1.27 - 1.41: 6367 1.41 - 1.54: 15005 1.54 - 1.68: 150 1.68 - 1.81: 192 Bond restraints: 25980 Sorted by residual: bond pdb=" CA ASP F 72 " pdb=" C ASP F 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.96e+01 bond pdb=" CA ASP C 72 " pdb=" C ASP C 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.95e+01 bond pdb=" CA ASP A 72 " pdb=" C ASP A 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.95e+01 bond pdb=" CA ASP B 72 " pdb=" C ASP B 72 " ideal model delta sigma weight residual 1.524 1.414 0.110 1.23e-02 6.61e+03 7.93e+01 bond pdb=" CA ASP E 72 " pdb=" C ASP E 72 " ideal model delta sigma weight residual 1.524 1.415 0.109 1.23e-02 6.61e+03 7.87e+01 ... (remaining 25975 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.72: 967 106.72 - 114.12: 14792 114.12 - 121.52: 13302 121.52 - 128.92: 5937 128.92 - 136.32: 240 Bond angle restraints: 35238 Sorted by residual: angle pdb=" N HIS C 448 " pdb=" CA HIS C 448 " pdb=" C HIS C 448 " ideal model delta sigma weight residual 114.04 100.45 13.59 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS D 448 " pdb=" CA HIS D 448 " pdb=" C HIS D 448 " ideal model delta sigma weight residual 114.04 100.46 13.58 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS B 448 " pdb=" CA HIS B 448 " pdb=" C HIS B 448 " ideal model delta sigma weight residual 114.04 100.47 13.57 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS A 448 " pdb=" CA HIS A 448 " pdb=" C HIS A 448 " ideal model delta sigma weight residual 114.04 100.48 13.56 1.24e+00 6.50e-01 1.20e+02 angle pdb=" N HIS E 448 " pdb=" CA HIS E 448 " pdb=" C HIS E 448 " ideal model delta sigma weight residual 114.04 100.49 13.55 1.24e+00 6.50e-01 1.19e+02 ... (remaining 35233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 15036 35.53 - 71.06: 477 71.06 - 106.59: 36 106.59 - 142.12: 0 142.12 - 177.65: 3 Dihedral angle restraints: 15552 sinusoidal: 6324 harmonic: 9228 Sorted by residual: dihedral pdb=" C5' AMP A 602 " pdb=" O5' AMP A 602 " pdb=" P AMP A 602 " pdb=" O3P AMP A 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.35 177.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' AMP C 602 " pdb=" O5' AMP C 602 " pdb=" P AMP C 602 " pdb=" O3P AMP C 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.36 177.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' AMP E 602 " pdb=" O5' AMP E 602 " pdb=" P AMP E 602 " pdb=" O3P AMP E 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.36 177.65 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 15549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 3649 0.129 - 0.258: 185 0.258 - 0.388: 84 0.388 - 0.517: 42 0.517 - 0.646: 24 Chirality restraints: 3984 Sorted by residual: chirality pdb=" CB VAL D 253 " pdb=" CA VAL D 253 " pdb=" CG1 VAL D 253 " pdb=" CG2 VAL D 253 " both_signs ideal model delta sigma weight residual False -2.63 -1.98 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CB VAL B 253 " pdb=" CA VAL B 253 " pdb=" CG1 VAL B 253 " pdb=" CG2 VAL B 253 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CB VAL E 253 " pdb=" CA VAL E 253 " pdb=" CG1 VAL E 253 " pdb=" CG2 VAL E 253 " both_signs ideal model delta sigma weight residual False -2.63 -1.99 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 3981 not shown) Planarity restraints: 4470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 338 " 0.022 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C GLU D 338 " -0.082 2.00e-02 2.50e+03 pdb=" O GLU D 338 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU D 339 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 338 " 0.022 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C GLU B 338 " -0.082 2.00e-02 2.50e+03 pdb=" O GLU B 338 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU B 339 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 338 " -0.022 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C GLU A 338 " 0.082 2.00e-02 2.50e+03 pdb=" O GLU A 338 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU A 339 " -0.028 2.00e-02 2.50e+03 ... (remaining 4467 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 738 2.68 - 3.24: 23664 3.24 - 3.79: 39263 3.79 - 4.35: 56676 4.35 - 4.90: 91592 Nonbonded interactions: 211933 Sorted by model distance: nonbonded pdb="MG MG B 601 " pdb=" O3P AMP B 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG D 601 " pdb=" O3P AMP D 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG A 601 " pdb=" O1P AMP A 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1P AMP C 602 " model vdw 2.130 2.170 nonbonded pdb="MG MG E 601 " pdb=" O1P AMP E 602 " model vdw 2.130 2.170 ... (remaining 211928 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 8.690 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 67.880 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.190 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:11.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 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 : 0.012 0.141 25980 Z= 0.789 Angle : 1.098 13.588 35238 Z= 0.684 Chirality : 0.100 0.646 3984 Planarity : 0.007 0.048 4470 Dihedral : 16.824 177.648 9612 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.49 % Favored : 91.32 % Rotamer: Outliers : 0.69 % Allowed : 20.01 % Favored : 79.30 % 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: -1.86 (0.14), residues: 3156 helix: -0.50 (0.16), residues: 1062 sheet: -0.60 (0.24), residues: 522 loop : -2.00 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 437 HIS 0.013 0.001 HIS F 408 PHE 0.007 0.001 PHE E 315 TYR 0.020 0.002 TYR F 174 ARG 0.007 0.000 ARG C 426 *********************** 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 259 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 240 time to evaluate : 3.046 Fit side-chains REVERT: A 367 MET cc_start: 0.8170 (mmm) cc_final: 0.7935 (mmm) REVERT: C 58 MET cc_start: 0.8321 (mtt) cc_final: 0.8055 (mtt) REVERT: C 224 MET cc_start: 0.8407 (ttt) cc_final: 0.7925 (ttt) REVERT: C 343 GLN cc_start: 0.8054 (tt0) cc_final: 0.7761 (mp10) REVERT: D 58 MET cc_start: 0.8302 (mtt) cc_final: 0.8035 (mtt) REVERT: D 224 MET cc_start: 0.8491 (ttt) cc_final: 0.7811 (ttt) REVERT: D 275 LEU cc_start: 0.8395 (mt) cc_final: 0.8093 (mp) REVERT: D 343 GLN cc_start: 0.8234 (tt0) cc_final: 0.7905 (mp10) REVERT: E 96 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7991 (mpt-90) REVERT: E 224 MET cc_start: 0.8355 (ttt) cc_final: 0.7990 (ttt) REVERT: F 342 ASP cc_start: 0.7504 (t0) cc_final: 0.7279 (t0) REVERT: F 343 GLN cc_start: 0.8027 (tt0) cc_final: 0.7733 (mm-40) REVERT: F 367 MET cc_start: 0.8176 (mmm) cc_final: 0.7957 (mmm) outliers start: 19 outliers final: 3 residues processed: 252 average time/residue: 1.3490 time to fit residues: 396.0503 Evaluate side-chains 193 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 190 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain E residue 275 LEU 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: 0.9980 chunk 131 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 148 optimal weight: 20.0000 chunk 182 optimal weight: 0.9980 chunk 283 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 29 GLN A 117 HIS A 206 ASN A 209 GLN A 213 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS B 12 GLN B 29 GLN B 117 HIS B 206 ASN B 209 GLN B 213 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS C 12 GLN C 29 GLN C 117 HIS C 206 ASN C 209 GLN C 213 HIS C 408 HIS D 12 GLN D 29 GLN D 117 HIS D 206 ASN D 209 GLN D 213 HIS D 408 HIS E 12 GLN E 29 GLN E 117 HIS E 206 ASN E 209 GLN E 213 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 HIS F 12 GLN F 29 GLN F 117 HIS F 206 ASN F 209 GLN F 213 HIS ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25980 Z= 0.176 Angle : 0.591 7.680 35238 Z= 0.298 Chirality : 0.047 0.150 3984 Planarity : 0.004 0.039 4470 Dihedral : 7.262 134.315 3504 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.64 % Favored : 92.17 % Rotamer: Outliers : 2.72 % Allowed : 18.92 % Favored : 78.36 % 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: -1.32 (0.15), residues: 3156 helix: 0.03 (0.16), residues: 1026 sheet: -0.77 (0.23), residues: 564 loop : -1.52 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 466 HIS 0.003 0.001 HIS C 36 PHE 0.007 0.001 PHE F 225 TYR 0.010 0.001 TYR D 174 ARG 0.003 0.000 ARG A 426 *********************** 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 292 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 217 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: A 281 LYS cc_start: 0.7418 (tttm) cc_final: 0.7208 (tttm) REVERT: B 343 GLN cc_start: 0.8217 (mp10) cc_final: 0.7947 (mp10) REVERT: C 224 MET cc_start: 0.8545 (ttt) cc_final: 0.8116 (ttt) REVERT: C 346 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: D 224 MET cc_start: 0.8683 (ttt) cc_final: 0.8238 (ttt) REVERT: D 275 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8061 (mp) REVERT: F 367 MET cc_start: 0.7886 (mmm) cc_final: 0.7358 (mmm) REVERT: F 464 ASN cc_start: 0.3106 (OUTLIER) cc_final: 0.2855 (p0) outliers start: 75 outliers final: 30 residues processed: 275 average time/residue: 1.2623 time to fit residues: 407.3676 Evaluate side-chains 225 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 192 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 449 GLN Chi-restraints excluded: chain F residue 464 ASN Chi-restraints excluded: chain F residue 469 VAL 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: 0.0870 chunk 235 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 283 optimal weight: 2.9990 chunk 306 optimal weight: 10.0000 chunk 252 optimal weight: 50.0000 chunk 281 optimal weight: 1.9990 chunk 96 optimal weight: 50.0000 chunk 227 optimal weight: 2.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25980 Z= 0.292 Angle : 0.626 7.708 35238 Z= 0.319 Chirality : 0.049 0.180 3984 Planarity : 0.004 0.043 4470 Dihedral : 6.806 104.555 3500 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.68 % Favored : 91.13 % Rotamer: Outliers : 3.78 % Allowed : 18.66 % Favored : 77.56 % 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: -1.32 (0.15), residues: 3156 helix: 0.06 (0.16), residues: 1038 sheet: -0.81 (0.22), residues: 558 loop : -1.53 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 290 HIS 0.005 0.001 HIS D 36 PHE 0.013 0.002 PHE B 315 TYR 0.013 0.002 TYR D 174 ARG 0.004 0.000 ARG A 96 *********************** 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 298 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 194 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.7652 (tttm) cc_final: 0.7252 (tttm) REVERT: B 226 HIS cc_start: 0.6569 (OUTLIER) cc_final: 0.6256 (m170) REVERT: B 238 MET cc_start: 0.8962 (ttt) cc_final: 0.8753 (ttt) REVERT: B 343 GLN cc_start: 0.8165 (mp10) cc_final: 0.7883 (mp10) REVERT: B 452 SER cc_start: 0.3962 (OUTLIER) cc_final: 0.3687 (t) REVERT: C 346 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6913 (tm-30) REVERT: D 158 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7702 (mt-10) REVERT: D 275 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8069 (mp) REVERT: D 346 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7003 (tm-30) REVERT: E 340 ASP cc_start: 0.7466 (p0) cc_final: 0.7144 (p0) REVERT: E 343 GLN cc_start: 0.7823 (mt0) cc_final: 0.7490 (mp10) REVERT: F 226 HIS cc_start: 0.6629 (OUTLIER) cc_final: 0.6323 (m170) REVERT: F 367 MET cc_start: 0.7966 (mmm) cc_final: 0.7327 (mmm) REVERT: F 417 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: F 464 ASN cc_start: 0.3326 (OUTLIER) cc_final: 0.2988 (p0) outliers start: 104 outliers final: 52 residues processed: 279 average time/residue: 1.2731 time to fit residues: 417.0650 Evaluate side-chains 239 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 178 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 226 HIS Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 449 GLN Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 464 ASN 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: 0.7980 chunk 147 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 301 optimal weight: 3.9990 chunk 148 optimal weight: 20.0000 chunk 269 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25980 Z= 0.260 Angle : 0.613 8.919 35238 Z= 0.311 Chirality : 0.048 0.173 3984 Planarity : 0.004 0.048 4470 Dihedral : 6.575 83.212 3500 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.68 % Favored : 91.13 % Rotamer: Outliers : 3.96 % Allowed : 18.95 % Favored : 77.09 % 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: -1.30 (0.15), residues: 3156 helix: 0.10 (0.16), residues: 1050 sheet: -0.82 (0.22), residues: 558 loop : -1.54 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 386 HIS 0.004 0.001 HIS B 36 PHE 0.011 0.001 PHE A 225 TYR 0.014 0.001 TYR D 174 ARG 0.005 0.000 ARG A 96 *********************** 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 302 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 193 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7331 (tmmt) REVERT: A 417 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7039 (m-30) REVERT: B 43 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8522 (m) REVERT: B 226 HIS cc_start: 0.6535 (OUTLIER) cc_final: 0.6232 (m170) REVERT: B 343 GLN cc_start: 0.8199 (mp10) cc_final: 0.7913 (mp10) REVERT: C 43 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8448 (m) REVERT: C 346 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: C 417 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7369 (m-30) REVERT: C 452 SER cc_start: 0.3407 (OUTLIER) cc_final: 0.3156 (t) REVERT: D 158 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: D 275 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8063 (mp) REVERT: D 346 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: E 43 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8535 (m) REVERT: E 337 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7923 (mp) REVERT: E 340 ASP cc_start: 0.7405 (p0) cc_final: 0.7071 (p0) REVERT: E 343 GLN cc_start: 0.7859 (mt0) cc_final: 0.7575 (mp-120) REVERT: E 426 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.5675 (mmt180) REVERT: F 417 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: F 464 ASN cc_start: 0.3299 (OUTLIER) cc_final: 0.2922 (p0) outliers start: 109 outliers final: 50 residues processed: 285 average time/residue: 1.2067 time to fit residues: 406.1978 Evaluate side-chains 251 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 185 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 426 ARG Chi-restraints excluded: chain E residue 440 SER Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 464 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 257 optimal weight: 0.0010 chunk 208 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25980 Z= 0.258 Angle : 0.607 7.941 35238 Z= 0.309 Chirality : 0.048 0.285 3984 Planarity : 0.004 0.046 4470 Dihedral : 6.522 66.025 3500 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.65 % Favored : 91.16 % Rotamer: Outliers : 3.70 % Allowed : 19.72 % Favored : 76.58 % 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: -1.27 (0.15), residues: 3156 helix: 0.13 (0.16), residues: 1050 sheet: -0.79 (0.22), residues: 558 loop : -1.54 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 437 HIS 0.004 0.001 HIS A 226 PHE 0.011 0.001 PHE F 225 TYR 0.015 0.001 TYR D 174 ARG 0.006 0.000 ARG A 96 *********************** 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 294 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 192 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8442 (m) REVERT: A 248 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7328 (tmmt) REVERT: A 417 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.6985 (m-30) REVERT: B 43 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8556 (m) REVERT: B 226 HIS cc_start: 0.6548 (OUTLIER) cc_final: 0.6233 (m170) REVERT: B 238 MET cc_start: 0.8926 (ttt) cc_final: 0.8706 (ttt) REVERT: B 337 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7862 (mp) REVERT: B 343 GLN cc_start: 0.8272 (mp10) cc_final: 0.7959 (mp10) REVERT: C 43 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8497 (m) REVERT: C 224 MET cc_start: 0.8492 (ttt) cc_final: 0.8044 (ttt) REVERT: C 346 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6909 (tm-30) REVERT: C 417 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7401 (m-30) REVERT: C 452 SER cc_start: 0.3379 (OUTLIER) cc_final: 0.3149 (t) REVERT: D 43 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8461 (m) REVERT: D 224 MET cc_start: 0.8695 (ttt) cc_final: 0.8360 (ttt) REVERT: D 275 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8062 (mp) REVERT: D 346 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: E 337 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7950 (mp) REVERT: E 340 ASP cc_start: 0.7558 (p0) cc_final: 0.6495 (p0) REVERT: E 343 GLN cc_start: 0.7829 (mt0) cc_final: 0.7400 (mp10) REVERT: F 417 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7322 (m-30) outliers start: 102 outliers final: 52 residues processed: 274 average time/residue: 1.1977 time to fit residues: 389.5886 Evaluate side-chains 252 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 185 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 440 SER Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 449 GLN Chi-restraints excluded: chain F residue 452 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 10.0000 chunk 271 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 177 optimal weight: 0.0770 chunk 74 optimal weight: 0.4980 chunk 301 optimal weight: 2.9990 chunk 250 optimal weight: 8.9990 chunk 139 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 HIS F 226 HIS ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25980 Z= 0.143 Angle : 0.553 10.473 35238 Z= 0.278 Chirality : 0.045 0.148 3984 Planarity : 0.004 0.051 4470 Dihedral : 6.333 59.500 3500 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.29 % Favored : 92.52 % Rotamer: Outliers : 2.40 % Allowed : 21.64 % Favored : 75.96 % 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: -1.10 (0.15), residues: 3156 helix: 0.29 (0.17), residues: 1056 sheet: -0.71 (0.22), residues: 564 loop : -1.44 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 290 HIS 0.003 0.001 HIS E 267 PHE 0.010 0.001 PHE C 225 TYR 0.008 0.001 TYR D 148 ARG 0.007 0.000 ARG A 96 *********************** 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 282 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 216 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 337 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7825 (mp) REVERT: B 343 GLN cc_start: 0.8206 (mp10) cc_final: 0.7891 (mp10) REVERT: C 172 THR cc_start: 0.8633 (m) cc_final: 0.8414 (p) REVERT: D 172 THR cc_start: 0.8673 (m) cc_final: 0.8451 (p) REVERT: D 275 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8052 (mp) REVERT: E 76 TYR cc_start: 0.9229 (OUTLIER) cc_final: 0.6653 (m-80) REVERT: E 337 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7905 (mp) REVERT: E 340 ASP cc_start: 0.7644 (p0) cc_final: 0.7365 (p0) REVERT: E 343 GLN cc_start: 0.7817 (mt0) cc_final: 0.7529 (mp-120) REVERT: F 464 ASN cc_start: 0.3177 (OUTLIER) cc_final: 0.2774 (p0) outliers start: 66 outliers final: 31 residues processed: 262 average time/residue: 1.2384 time to fit residues: 380.8322 Evaluate side-chains 223 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 464 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 3.9990 chunk 34 optimal weight: 0.0030 chunk 171 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 254 optimal weight: 30.0000 chunk 168 optimal weight: 3.9990 chunk 300 optimal weight: 6.9990 chunk 188 optimal weight: 0.3980 chunk 183 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS F 256 ASN ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 25980 Z= 0.298 Angle : 0.622 7.709 35238 Z= 0.318 Chirality : 0.049 0.169 3984 Planarity : 0.004 0.046 4470 Dihedral : 6.555 59.861 3500 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.52 % Favored : 91.29 % Rotamer: Outliers : 3.16 % Allowed : 21.39 % Favored : 75.45 % 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: -1.19 (0.15), residues: 3156 helix: 0.28 (0.17), residues: 1014 sheet: -0.71 (0.22), residues: 558 loop : -1.53 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 437 HIS 0.004 0.001 HIS B 36 PHE 0.012 0.002 PHE F 225 TYR 0.017 0.002 TYR D 174 ARG 0.006 0.000 ARG A 96 *********************** 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 268 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 181 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8507 (m) REVERT: A 417 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7052 (m-30) REVERT: B 238 MET cc_start: 0.8973 (ttt) cc_final: 0.8768 (ttt) REVERT: B 337 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7940 (mp) REVERT: B 343 GLN cc_start: 0.8271 (mp10) cc_final: 0.7937 (mp10) REVERT: C 226 HIS cc_start: 0.6486 (OUTLIER) cc_final: 0.6091 (m170) REVERT: C 452 SER cc_start: 0.3543 (OUTLIER) cc_final: 0.3302 (t) REVERT: D 275 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8083 (mp) REVERT: E 337 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8022 (mp) REVERT: E 340 ASP cc_start: 0.7790 (p0) cc_final: 0.7566 (p0) REVERT: E 343 GLN cc_start: 0.7788 (mt0) cc_final: 0.7381 (mp10) REVERT: F 461 MET cc_start: 0.3797 (tmm) cc_final: 0.3487 (tmm) outliers start: 87 outliers final: 45 residues processed: 248 average time/residue: 1.3046 time to fit residues: 379.5961 Evaluate side-chains 228 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 176 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 440 SER Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 176 THR 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 275 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 449 GLN 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: 0.9990 chunk 179 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 204 optimal weight: 30.0000 chunk 148 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 532 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25980 Z= 0.288 Angle : 0.624 11.425 35238 Z= 0.317 Chirality : 0.049 0.186 3984 Planarity : 0.004 0.049 4470 Dihedral : 6.570 59.394 3500 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.81 % Favored : 91.00 % Rotamer: Outliers : 3.12 % Allowed : 21.35 % Favored : 75.53 % 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 (0.15), residues: 3156 helix: 0.19 (0.17), residues: 1020 sheet: -0.72 (0.23), residues: 558 loop : -1.57 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 437 HIS 0.005 0.001 HIS B 267 PHE 0.011 0.002 PHE F 225 TYR 0.016 0.002 TYR D 174 ARG 0.006 0.000 ARG F 96 *********************** 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 260 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 174 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8477 (m) REVERT: A 248 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7313 (tmmt) REVERT: A 417 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7076 (m-30) REVERT: B 337 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7939 (mp) REVERT: B 343 GLN cc_start: 0.8281 (mp10) cc_final: 0.7953 (mp10) REVERT: D 43 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8435 (m) REVERT: D 275 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8067 (mp) REVERT: D 417 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7375 (m-30) REVERT: E 337 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8033 (mp) REVERT: E 340 ASP cc_start: 0.7832 (p0) cc_final: 0.7543 (p0) REVERT: E 343 GLN cc_start: 0.7786 (mt0) cc_final: 0.7368 (mp10) REVERT: E 452 SER cc_start: 0.3957 (OUTLIER) cc_final: 0.3746 (t) REVERT: F 464 ASN cc_start: 0.3250 (OUTLIER) cc_final: 0.2888 (p0) outliers start: 86 outliers final: 49 residues processed: 244 average time/residue: 1.3025 time to fit residues: 373.0505 Evaluate side-chains 235 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 176 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 440 SER Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 176 THR 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 275 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 449 GLN Chi-restraints excluded: chain F residue 464 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.8980 chunk 288 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 220 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 253 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 279 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25980 Z= 0.200 Angle : 0.585 8.310 35238 Z= 0.296 Chirality : 0.047 0.162 3984 Planarity : 0.004 0.045 4470 Dihedral : 6.345 57.144 3498 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.21 % Favored : 91.60 % Rotamer: Outliers : 2.29 % Allowed : 21.97 % Favored : 75.74 % 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: -1.14 (0.15), residues: 3156 helix: 0.25 (0.17), residues: 1026 sheet: -0.66 (0.23), residues: 558 loop : -1.46 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 437 HIS 0.004 0.001 HIS B 267 PHE 0.009 0.001 PHE B 315 TYR 0.009 0.001 TYR F 318 ARG 0.007 0.000 ARG F 96 *********************** 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 245 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 182 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7293 (tmmt) REVERT: B 76 TYR cc_start: 0.9261 (OUTLIER) cc_final: 0.6696 (m-80) REVERT: B 337 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7930 (mp) REVERT: B 343 GLN cc_start: 0.8266 (mp10) cc_final: 0.7920 (mp10) REVERT: D 275 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8064 (mp) REVERT: E 76 TYR cc_start: 0.9267 (OUTLIER) cc_final: 0.6742 (m-80) REVERT: E 337 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8013 (mp) REVERT: E 340 ASP cc_start: 0.7795 (p0) cc_final: 0.7555 (p0) REVERT: E 343 GLN cc_start: 0.7785 (mt0) cc_final: 0.7376 (mp10) REVERT: F 43 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8467 (m) REVERT: F 58 MET cc_start: 0.8306 (mtt) cc_final: 0.8020 (mtt) REVERT: F 464 ASN cc_start: 0.3204 (OUTLIER) cc_final: 0.2889 (p0) outliers start: 63 outliers final: 42 residues processed: 234 average time/residue: 1.3675 time to fit residues: 375.4780 Evaluate side-chains 220 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 170 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 449 GLN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 449 GLN Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 449 GLN Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 176 THR 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 275 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 449 GLN Chi-restraints excluded: chain F residue 464 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.6980 chunk 296 optimal weight: 0.0470 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 0.0050 chunk 205 optimal weight: 4.9990 chunk 310 optimal weight: 9.9990 chunk 286 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 151 optimal weight: 0.0370 overall best weight: 0.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 HIS ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 532 HIS ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25980 Z= 0.130 Angle : 0.541 7.197 35238 Z= 0.272 Chirality : 0.045 0.143 3984 Planarity : 0.004 0.041 4470 Dihedral : 6.058 59.325 3498 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.97 % Favored : 92.84 % Rotamer: Outliers : 1.60 % Allowed : 22.48 % Favored : 75.93 % 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: -0.86 (0.15), residues: 3156 helix: 0.53 (0.17), residues: 1044 sheet: -0.65 (0.23), residues: 564 loop : -1.28 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 290 HIS 0.004 0.001 HIS F 463 PHE 0.009 0.001 PHE C 225 TYR 0.008 0.001 TYR F 148 ARG 0.007 0.000 ARG A 96 ********************** 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 241 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 197 time to evaluate : 2.776 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8169 (mtt) cc_final: 0.7900 (mtt) REVERT: B 76 TYR cc_start: 0.9223 (OUTLIER) cc_final: 0.6706 (m-80) REVERT: B 337 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7877 (mp) REVERT: B 343 GLN cc_start: 0.8276 (mp10) cc_final: 0.7963 (mp10) REVERT: C 172 THR cc_start: 0.8585 (m) cc_final: 0.8368 (p) REVERT: D 172 THR cc_start: 0.8635 (m) cc_final: 0.8404 (p) REVERT: D 275 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8057 (mp) REVERT: E 76 TYR cc_start: 0.9240 (OUTLIER) cc_final: 0.6785 (m-80) REVERT: E 337 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7969 (mp) REVERT: E 340 ASP cc_start: 0.7786 (p0) cc_final: 0.6468 (p0) REVERT: E 343 GLN cc_start: 0.7763 (mt0) cc_final: 0.7343 (mp10) REVERT: F 58 MET cc_start: 0.8175 (mtt) cc_final: 0.7855 (mtt) REVERT: F 174 TYR cc_start: 0.7673 (m-80) cc_final: 0.7270 (m-80) outliers start: 44 outliers final: 27 residues processed: 227 average time/residue: 1.3273 time to fit residues: 350.6662 Evaluate side-chains 212 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 449 GLN Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 76 TYR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 253 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 228 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 0.6980 chunk 103 optimal weight: 0.0870 chunk 254 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.164852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116583 restraints weight = 28717.366| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.00 r_work: 0.3132 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25980 Z= 0.151 Angle : 0.562 11.031 35238 Z= 0.282 Chirality : 0.045 0.148 3984 Planarity : 0.004 0.049 4470 Dihedral : 6.038 59.622 3498 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.35 % Favored : 92.46 % Rotamer: Outliers : 1.38 % Allowed : 23.06 % Favored : 75.56 % 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: -0.80 (0.15), residues: 3156 helix: 0.56 (0.17), residues: 1050 sheet: -0.64 (0.23), residues: 564 loop : -1.22 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 437 HIS 0.004 0.001 HIS E 267 PHE 0.008 0.001 PHE C 225 TYR 0.008 0.001 TYR E 148 ARG 0.005 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7425.48 seconds wall clock time: 136 minutes 0.53 seconds (8160.53 seconds total)