Starting phenix.real_space_refine on Tue Feb 20 00:46:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i35_35144/02_2024/8i35_35144_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i35_35144/02_2024/8i35_35144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i35_35144/02_2024/8i35_35144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i35_35144/02_2024/8i35_35144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i35_35144/02_2024/8i35_35144_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i35_35144/02_2024/8i35_35144_neut_trim_updated.pdb" } resolution = 2.75 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= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 108 5.16 5 C 16266 2.51 5 N 4224 2.21 5 O 4728 1.98 5 H 744 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 163": "OD1" <-> "OD2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A ASP 445": "OD1" <-> "OD2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "F ASP 163": "OD1" <-> "OD2" Residue "F PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 365": "OE1" <-> "OE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F ASP 417": "OD1" <-> "OD2" Residue "F ASP 445": "OD1" <-> "OD2" Residue "F GLU 527": "OE1" <-> "OE2" Residue "E ASP 163": "OD1" <-> "OD2" Residue "E PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 365": "OE1" <-> "OE2" Residue "E GLU 379": "OE1" <-> "OE2" Residue "E ASP 417": "OD1" <-> "OD2" Residue "E ASP 445": "OD1" <-> "OD2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B ASP 417": "OD1" <-> "OD2" Residue "B ASP 445": "OD1" <-> "OD2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C ASP 417": "OD1" <-> "OD2" Residue "C ASP 445": "OD1" <-> "OD2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "D ASP 163": "OD1" <-> "OD2" Residue "D PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 365": "OE1" <-> "OE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D ASP 417": "OD1" <-> "OD2" Residue "D ASP 445": "OD1" <-> "OD2" Residue "D 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: 26070 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4325 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: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4325 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: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4325 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: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4325 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: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4325 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: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4325 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: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.80, per 1000 atoms: 0.49 Number of scatterers: 26070 At special positions: 0 Unit cell: (169.338, 157.17, 94.302, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 O 4728 8.00 N 4224 7.00 C 16266 6.00 H 744 1.00 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=0, symmetry=0 Time building additional restraints: 9.87 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: 120 helices and 36 sheets defined 32.0% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.44 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.991A 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: 3.699A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 118 through 126 Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 229 through 239 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.548A pdb=" N LEU A 255 " --> pdb=" O PRO A 251 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 341 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 441 through 448 removed outlier: 3.621A pdb=" N ASP A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 493 removed outlier: 3.557A pdb=" N ASP A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'F' and resid 15 through 20 removed outlier: 3.991A 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: 3.699A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 99 through 109 Processing helix chain 'F' and resid 118 through 126 Proline residue: F 122 - end of helix Processing helix chain 'F' and resid 128 through 130 No H-bonds generated for 'chain 'F' and resid 128 through 130' Processing helix chain 'F' and resid 147 through 153 Processing helix chain 'F' and resid 189 through 203 Processing helix chain 'F' and resid 229 through 239 Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 251 through 261 removed outlier: 3.547A pdb=" N LEU F 255 " --> pdb=" O PRO F 251 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN F 256 " --> pdb=" O ASP F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 277 Processing helix chain 'F' and resid 282 through 284 No H-bonds generated for 'chain 'F' and resid 282 through 284' Processing helix chain 'F' and resid 301 through 309 Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 341 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 441 through 448 removed outlier: 3.622A pdb=" N ASP F 445 " --> pdb=" O LEU F 441 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE F 446 " --> pdb=" O GLU F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 493 removed outlier: 3.557A pdb=" N ASP F 493 " --> pdb=" O GLY F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 532 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.991A 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: 3.699A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 99 through 109 Processing helix chain 'E' and resid 118 through 126 Proline residue: E 122 - end of helix Processing helix chain 'E' and resid 128 through 130 No H-bonds generated for 'chain 'E' and resid 128 through 130' Processing helix chain 'E' and resid 147 through 153 Processing helix chain 'E' and resid 189 through 203 Processing helix chain 'E' and resid 229 through 239 Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 251 through 261 removed outlier: 3.548A pdb=" N LEU E 255 " --> pdb=" O PRO E 251 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN E 256 " --> pdb=" O ASP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 277 Processing helix chain 'E' and resid 282 through 284 No H-bonds generated for 'chain 'E' and resid 282 through 284' Processing helix chain 'E' and resid 301 through 309 Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 341 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 441 through 448 removed outlier: 3.622A pdb=" N ASP E 445 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE E 446 " --> pdb=" O GLU E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 493 removed outlier: 3.558A pdb=" N ASP E 493 " --> pdb=" O GLY E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 532 Processing helix chain 'B' and resid 15 through 20 removed outlier: 3.991A 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: 3.700A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 118 through 126 Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 189 through 203 Processing helix chain 'B' and resid 229 through 239 Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 251 through 261 removed outlier: 3.548A pdb=" N LEU B 255 " --> pdb=" O PRO B 251 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 277 Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 341 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 441 through 448 removed outlier: 3.621A pdb=" N ASP B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 493 removed outlier: 3.557A pdb=" N ASP B 493 " --> pdb=" O GLY B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 532 Processing helix chain 'C' and resid 15 through 20 removed outlier: 3.990A 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: 3.699A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 118 through 126 Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 229 through 239 Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 251 through 261 removed outlier: 3.547A pdb=" N LEU C 255 " --> pdb=" O PRO C 251 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 277 Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 301 through 309 Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 341 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 441 through 448 removed outlier: 3.621A pdb=" N ASP C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 446 " --> pdb=" O GLU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 493 removed outlier: 3.557A pdb=" N ASP C 493 " --> pdb=" O GLY C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 532 Processing helix chain 'D' and resid 15 through 20 removed outlier: 3.991A 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: 3.699A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 118 through 126 Proline residue: D 122 - end of helix Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 189 through 203 Processing helix chain 'D' and resid 229 through 239 Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 251 through 261 removed outlier: 3.547A pdb=" N LEU D 255 " --> pdb=" O PRO D 251 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 277 Processing helix chain 'D' and resid 282 through 284 No H-bonds generated for 'chain 'D' and resid 282 through 284' Processing helix chain 'D' and resid 301 through 309 Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 341 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 441 through 448 removed outlier: 3.622A pdb=" N ASP D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE D 446 " --> pdb=" O GLU D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 493 removed outlier: 3.557A pdb=" N ASP D 493 " --> pdb=" O GLY D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 532 Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.467A pdb=" N GLN A 243 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE A 265 " --> pdb=" O MET A 219 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS A 291 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N CYS A 268 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL A 293 " --> pdb=" O CYS A 268 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 89 through 92 removed outlier: 6.526A pdb=" N ILE A 113 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N MET A 69 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 115 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG A 136 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE A 116 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.813A 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 169 through 172 removed outlier: 6.822A pdb=" N PHE A 187 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 411 through 415 removed outlier: 6.699A pdb=" N HIS A 414 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE A 423 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 453 through 461 removed outlier: 6.705A pdb=" N THR A 475 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL A 456 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A 473 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL A 458 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 471 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY A 460 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL A 469 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.467A pdb=" N GLN F 243 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE F 265 " --> pdb=" O MET F 219 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LYS F 291 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N CYS F 268 " --> pdb=" O LYS F 291 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL F 293 " --> pdb=" O CYS F 268 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 89 through 92 removed outlier: 6.526A pdb=" N ILE F 113 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N MET F 69 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU F 115 " --> pdb=" O MET F 69 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG F 136 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE F 116 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL F 138 " --> pdb=" O ILE F 116 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 361 through 363 Processing sheet with id= J, first strand: chain 'F' and resid 169 through 172 removed outlier: 6.822A pdb=" N PHE F 187 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 411 through 415 removed outlier: 6.699A pdb=" N HIS F 414 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE F 423 " --> pdb=" O HIS F 414 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 453 through 461 removed outlier: 6.705A pdb=" N THR F 475 " --> pdb=" O SER F 454 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL F 456 " --> pdb=" O LEU F 473 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU F 473 " --> pdb=" O VAL F 456 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL F 458 " --> pdb=" O LEU F 471 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU F 471 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY F 460 " --> pdb=" O VAL F 469 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL F 469 " --> pdb=" O GLY F 460 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.467A pdb=" N GLN E 243 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE E 265 " --> pdb=" O MET E 219 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS E 291 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N CYS E 268 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL E 293 " --> pdb=" O CYS E 268 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 89 through 92 removed outlier: 6.526A pdb=" N ILE E 113 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N MET E 69 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU E 115 " --> pdb=" O MET E 69 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG E 136 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE E 116 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL E 138 " --> pdb=" O ILE E 116 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 361 through 363 Processing sheet with id= P, first strand: chain 'E' and resid 169 through 172 removed outlier: 6.822A pdb=" N PHE E 187 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 411 through 415 removed outlier: 6.700A pdb=" N HIS E 414 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE E 423 " --> pdb=" O HIS E 414 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 453 through 461 removed outlier: 6.705A pdb=" N THR E 475 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL E 456 " --> pdb=" O LEU E 473 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU E 473 " --> pdb=" O VAL E 456 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL E 458 " --> pdb=" O LEU E 471 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU E 471 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY E 460 " --> pdb=" O VAL E 469 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL E 469 " --> pdb=" O GLY E 460 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.467A pdb=" N GLN B 243 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE B 265 " --> pdb=" O MET B 219 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS B 291 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N CYS B 268 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL B 293 " --> pdb=" O CYS B 268 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 89 through 92 removed outlier: 6.526A pdb=" N ILE B 113 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N MET B 69 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 115 " --> pdb=" O MET B 69 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG B 136 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE B 116 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL B 138 " --> pdb=" O ILE B 116 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 361 through 363 Processing sheet with id= V, first strand: chain 'B' and resid 169 through 172 removed outlier: 6.822A pdb=" N PHE B 187 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 411 through 415 removed outlier: 6.699A pdb=" N HIS B 414 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE B 423 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 453 through 461 removed outlier: 6.704A pdb=" N THR B 475 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B 456 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 473 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL B 458 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 471 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY B 460 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL B 469 " --> pdb=" O GLY B 460 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.466A pdb=" N GLN C 243 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE C 265 " --> pdb=" O MET C 219 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS C 291 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N CYS C 268 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL C 293 " --> pdb=" O CYS C 268 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 89 through 92 removed outlier: 6.525A pdb=" N ILE C 113 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N MET C 69 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU C 115 " --> pdb=" O MET C 69 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG C 136 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE C 116 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL C 138 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 361 through 363 Processing sheet with id= AB, first strand: chain 'C' and resid 169 through 172 removed outlier: 6.822A pdb=" N PHE C 187 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 411 through 415 removed outlier: 6.699A pdb=" N HIS C 414 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE C 423 " --> pdb=" O HIS C 414 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 453 through 461 removed outlier: 6.706A pdb=" N THR C 475 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL C 456 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU C 473 " --> pdb=" O VAL C 456 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL C 458 " --> pdb=" O LEU C 471 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU C 471 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY C 460 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL C 469 " --> pdb=" O GLY C 460 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.467A pdb=" N GLN D 243 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE D 265 " --> pdb=" O MET D 219 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS D 291 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N CYS D 268 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL D 293 " --> pdb=" O CYS D 268 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 89 through 92 removed outlier: 6.526A pdb=" N ILE D 113 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N MET D 69 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU D 115 " --> pdb=" O MET D 69 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG D 136 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE D 116 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL D 138 " --> pdb=" O ILE D 116 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 361 through 363 Processing sheet with id= AH, first strand: chain 'D' and resid 169 through 172 removed outlier: 6.822A pdb=" N PHE D 187 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 411 through 415 removed outlier: 6.698A pdb=" N HIS D 414 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE D 423 " --> pdb=" O HIS D 414 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'D' and resid 453 through 461 removed outlier: 6.704A pdb=" N THR D 475 " --> pdb=" O SER D 454 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL D 456 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU D 473 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL D 458 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU D 471 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY D 460 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL D 469 " --> pdb=" O GLY D 460 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1494 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: 8.13 Time building geometry restraints manager: 10.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 744 1.02 - 1.21: 75 1.21 - 1.41: 10425 1.41 - 1.61: 15192 1.61 - 1.81: 192 Bond restraints: 26628 Sorted by residual: bond pdb=" C10 OLA F1001 " pdb=" C9 OLA F1001 " ideal model delta sigma weight residual 1.332 1.519 -0.187 2.00e-02 2.50e+03 8.78e+01 bond pdb=" C10 OLA E1001 " pdb=" C9 OLA E1001 " ideal model delta sigma weight residual 1.332 1.519 -0.187 2.00e-02 2.50e+03 8.77e+01 bond pdb=" C10 OLA A1001 " pdb=" C9 OLA A1001 " ideal model delta sigma weight residual 1.332 1.519 -0.187 2.00e-02 2.50e+03 8.76e+01 bond pdb=" C10 OLA B1001 " pdb=" C9 OLA B1001 " ideal model delta sigma weight residual 1.332 1.519 -0.187 2.00e-02 2.50e+03 8.76e+01 bond pdb=" C10 OLA C1001 " pdb=" C9 OLA C1001 " ideal model delta sigma weight residual 1.332 1.519 -0.187 2.00e-02 2.50e+03 8.70e+01 ... (remaining 26623 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.66: 525 105.66 - 113.21: 15905 113.21 - 120.76: 11723 120.76 - 128.31: 8365 128.31 - 135.86: 238 Bond angle restraints: 36756 Sorted by residual: angle pdb=" N ILE F 433 " pdb=" CA ILE F 433 " pdb=" CB ILE F 433 " ideal model delta sigma weight residual 110.49 117.02 -6.53 1.15e+00 7.56e-01 3.23e+01 angle pdb=" N ILE E 433 " pdb=" CA ILE E 433 " pdb=" CB ILE E 433 " ideal model delta sigma weight residual 110.49 117.01 -6.52 1.15e+00 7.56e-01 3.22e+01 angle pdb=" N ILE C 433 " pdb=" CA ILE C 433 " pdb=" CB ILE C 433 " ideal model delta sigma weight residual 110.49 116.98 -6.49 1.15e+00 7.56e-01 3.19e+01 angle pdb=" N ILE A 433 " pdb=" CA ILE A 433 " pdb=" CB ILE A 433 " ideal model delta sigma weight residual 110.49 116.98 -6.49 1.15e+00 7.56e-01 3.19e+01 angle pdb=" N ILE B 433 " pdb=" CA ILE B 433 " pdb=" CB ILE B 433 " ideal model delta sigma weight residual 110.49 116.98 -6.49 1.15e+00 7.56e-01 3.19e+01 ... (remaining 36751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13643 17.97 - 35.95: 1567 35.95 - 53.92: 444 53.92 - 71.89: 84 71.89 - 89.86: 30 Dihedral angle restraints: 15768 sinusoidal: 6522 harmonic: 9246 Sorted by residual: dihedral pdb=" CA HIS C 532 " pdb=" C HIS C 532 " pdb=" N LEU C 533 " pdb=" CA LEU C 533 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA HIS F 532 " pdb=" C HIS F 532 " pdb=" N LEU F 533 " pdb=" CA LEU F 533 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA HIS B 532 " pdb=" C HIS B 532 " pdb=" N LEU B 533 " pdb=" CA LEU B 533 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 15765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3306 0.073 - 0.146: 577 0.146 - 0.219: 35 0.219 - 0.292: 24 0.292 - 0.365: 18 Chirality restraints: 3960 Sorted by residual: chirality pdb=" CA THR F 196 " pdb=" N THR F 196 " pdb=" C THR F 196 " pdb=" CB THR F 196 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA THR D 196 " pdb=" N THR D 196 " pdb=" C THR D 196 " pdb=" CB THR D 196 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA THR A 196 " pdb=" N THR A 196 " pdb=" C THR A 196 " pdb=" CB THR A 196 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3957 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA E1001 " 0.242 2.00e-02 2.50e+03 1.90e-01 3.62e+02 pdb=" C11 OLA E1001 " -0.117 2.00e-02 2.50e+03 pdb=" C8 OLA E1001 " 0.118 2.00e-02 2.50e+03 pdb=" C9 OLA E1001 " -0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA F1001 " -0.241 2.00e-02 2.50e+03 1.90e-01 3.62e+02 pdb=" C11 OLA F1001 " 0.117 2.00e-02 2.50e+03 pdb=" C8 OLA F1001 " -0.118 2.00e-02 2.50e+03 pdb=" C9 OLA F1001 " 0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA A1001 " 0.241 2.00e-02 2.50e+03 1.90e-01 3.62e+02 pdb=" C11 OLA A1001 " -0.117 2.00e-02 2.50e+03 pdb=" C8 OLA A1001 " 0.118 2.00e-02 2.50e+03 pdb=" C9 OLA A1001 " -0.243 2.00e-02 2.50e+03 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.39: 528 2.39 - 2.94: 13883 2.94 - 3.49: 31229 3.49 - 4.05: 52603 4.05 - 4.60: 78387 Nonbonded interactions: 176630 Sorted by model distance: nonbonded pdb=" HA ILE F 199 " pdb="HG22 THR F 202 " model vdw 1.834 2.440 nonbonded pdb=" HA ILE C 199 " pdb="HG22 THR C 202 " model vdw 1.834 2.440 nonbonded pdb=" HA ILE A 199 " pdb="HG22 THR A 202 " model vdw 1.835 2.440 nonbonded pdb=" HA ILE B 199 " pdb="HG22 THR B 202 " model vdw 1.835 2.440 nonbonded pdb=" HA ILE D 199 " pdb="HG22 THR D 202 " model vdw 1.835 2.440 ... (remaining 176625 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.660 Extract box with map and model: 8.580 Check model and map are aligned: 0.390 Set scattering table: 0.210 Process input model: 65.840 Find NCS groups from input model: 1.760 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:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.187 25884 Z= 0.450 Angle : 0.894 14.556 35064 Z= 0.490 Chirality : 0.059 0.365 3960 Planarity : 0.009 0.190 4470 Dihedral : 16.847 89.863 9612 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.65 % Favored : 91.16 % Rotamer: Outliers : 0.29 % Allowed : 20.62 % Favored : 79.08 % 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: -1.50 (0.15), residues: 3156 helix: -0.12 (0.16), residues: 1068 sheet: -0.80 (0.22), residues: 558 loop : -1.70 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 386 HIS 0.015 0.002 HIS E 213 PHE 0.012 0.002 PHE C 161 TYR 0.015 0.002 TYR C 148 ARG 0.002 0.000 ARG C 37 *********************** 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 211 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 203 time to evaluate : 2.225 Fit side-chains REVERT: A 238 MET cc_start: 0.9220 (tpp) cc_final: 0.8439 (tpt) REVERT: A 399 LYS cc_start: 0.8955 (mtpm) cc_final: 0.8371 (mttp) REVERT: F 379 GLU cc_start: 0.8762 (tt0) cc_final: 0.8520 (tt0) REVERT: F 425 ASP cc_start: 0.7911 (t0) cc_final: 0.7616 (t0) REVERT: E 107 ASP cc_start: 0.8421 (t70) cc_final: 0.8172 (t70) REVERT: B 238 MET cc_start: 0.9191 (tpp) cc_final: 0.8424 (tpt) REVERT: C 425 ASP cc_start: 0.7968 (t0) cc_final: 0.7685 (t0) REVERT: D 107 ASP cc_start: 0.8443 (t70) cc_final: 0.8191 (t70) outliers start: 8 outliers final: 2 residues processed: 211 average time/residue: 1.4224 time to fit residues: 340.4092 Evaluate side-chains 172 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain B residue 128 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 chunk 131 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 244 optimal weight: 0.2980 chunk 94 optimal weight: 9.9990 chunk 148 optimal weight: 20.0000 chunk 182 optimal weight: 3.9990 chunk 283 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN A 12 GLN A 29 GLN A 117 HIS A 154 GLN A 206 ASN A 213 HIS A 228 HIS ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS A 274 HIS A 408 HIS F 6 ASN F 12 GLN F 29 GLN F 117 HIS F 154 GLN F 206 ASN F 213 HIS F 228 HIS ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 HIS F 274 HIS F 408 HIS E 6 ASN E 12 GLN E 29 GLN E 117 HIS E 154 GLN E 206 ASN E 213 HIS E 228 HIS ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 HIS E 274 HIS E 408 HIS B 6 ASN B 12 GLN B 29 GLN B 117 HIS B 154 GLN B 206 ASN B 213 HIS B 228 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS B 274 HIS B 408 HIS C 6 ASN C 12 GLN C 29 GLN C 117 HIS C 154 GLN C 206 ASN C 213 HIS C 228 HIS ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS C 274 HIS C 408 HIS D 6 ASN D 12 GLN D 29 GLN D 117 HIS D 154 GLN D 206 ASN D 213 HIS D 228 HIS D 267 HIS D 274 HIS D 408 HIS Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 25884 Z= 0.128 Angle : 0.437 4.096 35064 Z= 0.234 Chirality : 0.043 0.136 3960 Planarity : 0.003 0.032 4470 Dihedral : 7.857 79.033 3506 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.27 % Favored : 93.54 % Rotamer: Outliers : 1.38 % Allowed : 20.73 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.15), residues: 3156 helix: 0.37 (0.17), residues: 1092 sheet: -0.82 (0.23), residues: 576 loop : -1.62 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 290 HIS 0.005 0.001 HIS D 228 PHE 0.008 0.001 PHE E 225 TYR 0.010 0.001 TYR A 148 ARG 0.001 0.000 ARG C 502 *********************** 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 240 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 202 time to evaluate : 3.549 Fit side-chains REVERT: A 379 GLU cc_start: 0.8590 (tt0) cc_final: 0.8371 (tt0) REVERT: F 425 ASP cc_start: 0.7879 (t0) cc_final: 0.7605 (t0) REVERT: E 107 ASP cc_start: 0.8371 (t70) cc_final: 0.8130 (t70) REVERT: C 425 ASP cc_start: 0.7932 (t0) cc_final: 0.7670 (t0) REVERT: D 107 ASP cc_start: 0.8372 (t70) cc_final: 0.8132 (t70) REVERT: D 461 MET cc_start: 0.4771 (mtt) cc_final: 0.4007 (ttt) outliers start: 38 outliers final: 8 residues processed: 239 average time/residue: 1.4047 time to fit residues: 390.8216 Evaluate side-chains 194 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 186 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 112 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.1980 chunk 87 optimal weight: 4.9990 chunk 235 optimal weight: 0.0970 chunk 192 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 306 optimal weight: 10.0000 chunk 252 optimal weight: 20.0000 chunk 281 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 227 optimal weight: 2.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN F 154 GLN E 154 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN D 154 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 25884 Z= 0.228 Angle : 0.483 5.083 35064 Z= 0.257 Chirality : 0.045 0.151 3960 Planarity : 0.003 0.032 4470 Dihedral : 7.718 73.850 3498 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.86 % Favored : 91.95 % Rotamer: Outliers : 2.32 % Allowed : 20.01 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.15), residues: 3156 helix: 0.38 (0.17), residues: 1104 sheet: -0.62 (0.23), residues: 558 loop : -1.56 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 290 HIS 0.006 0.001 HIS A 228 PHE 0.012 0.001 PHE D 225 TYR 0.014 0.001 TYR D 148 ARG 0.002 0.000 ARG B 49 *********************** 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 246 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 182 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8600 (m) REVERT: F 314 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8624 (m) REVERT: F 500 LEU cc_start: 0.4443 (OUTLIER) cc_final: 0.4206 (mt) REVERT: E 107 ASP cc_start: 0.8377 (t70) cc_final: 0.8120 (t70) REVERT: E 232 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8837 (mm) REVERT: E 314 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8665 (m) REVERT: B 107 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7711 (t70) REVERT: B 314 VAL cc_start: 0.8871 (OUTLIER) cc_final: 0.8596 (m) REVERT: B 431 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.7132 (mp) REVERT: C 314 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8657 (m) REVERT: C 425 ASP cc_start: 0.7938 (t0) cc_final: 0.7671 (t0) REVERT: D 107 ASP cc_start: 0.8403 (t70) cc_final: 0.8147 (t70) REVERT: D 232 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8813 (mm) REVERT: D 314 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8693 (m) outliers start: 64 outliers final: 8 residues processed: 239 average time/residue: 1.3733 time to fit residues: 383.7455 Evaluate side-chains 195 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 329 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 135 optimal weight: 0.0370 chunk 190 optimal weight: 5.9990 chunk 284 optimal weight: 0.0870 chunk 301 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 81 optimal weight: 0.0040 overall best weight: 0.5850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN F 154 GLN E 154 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN D 154 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 25884 Z= 0.114 Angle : 0.408 4.381 35064 Z= 0.215 Chirality : 0.043 0.133 3960 Planarity : 0.003 0.025 4470 Dihedral : 7.139 65.612 3498 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.12 % Favored : 93.69 % Rotamer: Outliers : 1.20 % Allowed : 20.59 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 3156 helix: 0.73 (0.17), residues: 1104 sheet: -0.72 (0.23), residues: 576 loop : -1.40 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 290 HIS 0.003 0.001 HIS B 39 PHE 0.006 0.001 PHE A 173 TYR 0.010 0.001 TYR A 148 ARG 0.001 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 204 time to evaluate : 2.781 Fit side-chains REVERT: A 203 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8372 (tt) REVERT: A 379 GLU cc_start: 0.8642 (tt0) cc_final: 0.8381 (tt0) REVERT: A 431 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.7029 (mp) REVERT: F 314 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8593 (m) REVERT: F 365 GLU cc_start: 0.7651 (mp0) cc_final: 0.7385 (mp0) REVERT: E 107 ASP cc_start: 0.8350 (t70) cc_final: 0.8093 (t70) REVERT: B 107 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7673 (t70) REVERT: B 203 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8355 (tt) REVERT: C 203 ILE cc_start: 0.9061 (tt) cc_final: 0.8856 (pt) REVERT: C 314 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8600 (m) REVERT: C 425 ASP cc_start: 0.7949 (t0) cc_final: 0.7666 (t0) REVERT: D 107 ASP cc_start: 0.8373 (t70) cc_final: 0.8105 (t70) REVERT: D 320 MET cc_start: 0.6989 (ttt) cc_final: 0.6629 (ttt) outliers start: 33 outliers final: 10 residues processed: 234 average time/residue: 1.4011 time to fit residues: 384.7621 Evaluate side-chains 208 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 283 LYS Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 271 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.0070 chunk 171 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 257 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 153 optimal weight: 0.0870 chunk 270 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 GLN ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25884 Z= 0.245 Angle : 0.484 4.710 35064 Z= 0.256 Chirality : 0.045 0.149 3960 Planarity : 0.003 0.032 4470 Dihedral : 7.590 59.343 3498 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.21 % Favored : 91.60 % Rotamer: Outliers : 2.03 % Allowed : 20.48 % Favored : 77.49 % 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: -0.92 (0.15), residues: 3156 helix: 0.54 (0.17), residues: 1104 sheet: -0.82 (0.23), residues: 588 loop : -1.40 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 290 HIS 0.008 0.001 HIS A 228 PHE 0.012 0.001 PHE D 225 TYR 0.014 0.001 TYR A 148 ARG 0.002 0.000 ARG E 49 *********************** 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 235 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 179 time to evaluate : 3.060 Fit side-chains revert: symmetry clash REVERT: A 314 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8607 (m) REVERT: A 431 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7140 (mp) REVERT: F 62 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8060 (ttpt) REVERT: F 259 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: F 314 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8654 (m) REVERT: F 365 GLU cc_start: 0.7580 (mp0) cc_final: 0.7202 (mp0) REVERT: F 500 LEU cc_start: 0.4545 (OUTLIER) cc_final: 0.4276 (mp) REVERT: E 107 ASP cc_start: 0.8385 (t70) cc_final: 0.8119 (t70) REVERT: E 314 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8694 (m) REVERT: B 314 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8600 (m) REVERT: C 203 ILE cc_start: 0.9241 (tt) cc_final: 0.8877 (pt) REVERT: C 259 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: C 314 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8673 (m) REVERT: C 365 GLU cc_start: 0.7606 (mp0) cc_final: 0.7290 (mp0) REVERT: C 425 ASP cc_start: 0.7931 (t0) cc_final: 0.7675 (t0) REVERT: C 431 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6926 (mp) REVERT: D 107 ASP cc_start: 0.8394 (t70) cc_final: 0.8129 (t70) REVERT: D 314 VAL cc_start: 0.8988 (OUTLIER) cc_final: 0.8699 (m) outliers start: 56 outliers final: 16 residues processed: 228 average time/residue: 1.3416 time to fit residues: 356.7485 Evaluate side-chains 208 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 427 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 30.0000 chunk 271 optimal weight: 0.2980 chunk 59 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 301 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 99 optimal weight: 30.0000 chunk 158 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 GLN ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 25884 Z= 0.301 Angle : 0.521 4.956 35064 Z= 0.277 Chirality : 0.047 0.174 3960 Planarity : 0.004 0.034 4470 Dihedral : 7.815 59.608 3498 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.17 % Favored : 91.63 % Rotamer: Outliers : 1.92 % Allowed : 20.70 % Favored : 77.38 % 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: -1.05 (0.15), residues: 3156 helix: 0.40 (0.17), residues: 1068 sheet: -0.73 (0.23), residues: 558 loop : -1.45 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 386 HIS 0.007 0.001 HIS B 228 PHE 0.012 0.002 PHE D 225 TYR 0.014 0.002 TYR D 148 ARG 0.002 0.000 ARG C 502 *********************** 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 229 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 176 time to evaluate : 3.056 Fit side-chains REVERT: A 314 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8591 (m) REVERT: A 431 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.7135 (mp) REVERT: F 62 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7894 (ttpt) REVERT: F 259 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: F 314 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8672 (m) REVERT: F 365 GLU cc_start: 0.7707 (mp0) cc_final: 0.7465 (mp0) REVERT: E 107 ASP cc_start: 0.8408 (t70) cc_final: 0.8149 (t70) REVERT: E 314 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8693 (m) REVERT: B 238 MET cc_start: 0.9084 (tpt) cc_final: 0.8345 (tpt) REVERT: B 314 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8579 (m) REVERT: C 259 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: C 365 GLU cc_start: 0.7674 (mp0) cc_final: 0.7464 (mp0) REVERT: C 425 ASP cc_start: 0.7874 (t0) cc_final: 0.7654 (t0) REVERT: C 431 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7178 (mp) REVERT: D 107 ASP cc_start: 0.8413 (t70) cc_final: 0.8164 (t70) REVERT: D 314 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8703 (m) outliers start: 53 outliers final: 21 residues processed: 225 average time/residue: 1.3596 time to fit residues: 358.6269 Evaluate side-chains 200 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 169 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 427 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 254 optimal weight: 20.0000 chunk 168 optimal weight: 0.8980 chunk 300 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN F 154 GLN ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 25884 Z= 0.227 Angle : 0.473 4.615 35064 Z= 0.251 Chirality : 0.045 0.155 3960 Planarity : 0.003 0.033 4470 Dihedral : 7.323 59.729 3498 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.92 % Favored : 91.89 % Rotamer: Outliers : 1.82 % Allowed : 20.70 % Favored : 77.49 % 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: -0.95 (0.15), residues: 3156 helix: 0.50 (0.17), residues: 1104 sheet: -0.73 (0.23), residues: 558 loop : -1.44 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 386 HIS 0.005 0.001 HIS A 228 PHE 0.010 0.001 PHE D 225 TYR 0.013 0.001 TYR A 148 ARG 0.002 0.000 ARG B 37 *********************** 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 222 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 172 time to evaluate : 2.753 Fit side-chains revert: symmetry clash REVERT: A 314 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8583 (m) REVERT: F 259 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: F 314 VAL cc_start: 0.8891 (OUTLIER) cc_final: 0.8649 (m) REVERT: F 365 GLU cc_start: 0.7610 (mp0) cc_final: 0.7397 (mp0) REVERT: E 107 ASP cc_start: 0.8387 (t70) cc_final: 0.8139 (t70) REVERT: E 314 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8685 (m) REVERT: B 107 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7744 (t70) REVERT: B 314 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8575 (m) REVERT: C 259 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: C 314 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8673 (m) REVERT: C 365 GLU cc_start: 0.7585 (mp0) cc_final: 0.7268 (mp0) REVERT: C 425 ASP cc_start: 0.7891 (t0) cc_final: 0.7633 (t0) REVERT: D 107 ASP cc_start: 0.8405 (t70) cc_final: 0.8144 (t70) REVERT: D 314 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8699 (m) outliers start: 50 outliers final: 23 residues processed: 218 average time/residue: 1.4236 time to fit residues: 359.6800 Evaluate side-chains 199 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 427 VAL 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: 0.0970 chunk 179 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 236 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 25884 Z= 0.118 Angle : 0.405 4.196 35064 Z= 0.213 Chirality : 0.043 0.135 3960 Planarity : 0.003 0.025 4470 Dihedral : 6.785 59.819 3498 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 24.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.46 % Favored : 93.35 % Rotamer: Outliers : 1.31 % Allowed : 21.39 % Favored : 77.31 % 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: -0.68 (0.16), residues: 3156 helix: 0.86 (0.17), residues: 1104 sheet: -0.79 (0.23), residues: 576 loop : -1.30 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 290 HIS 0.003 0.001 HIS B 39 PHE 0.006 0.001 PHE C 161 TYR 0.009 0.001 TYR B 148 ARG 0.001 0.000 ARG B 211 *********************** 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 225 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 189 time to evaluate : 2.941 Fit side-chains REVERT: A 314 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8534 (m) REVERT: F 259 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: F 314 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8621 (m) REVERT: F 365 GLU cc_start: 0.7681 (mp0) cc_final: 0.7340 (mp0) REVERT: F 430 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7665 (mmm) REVERT: E 107 ASP cc_start: 0.8373 (t70) cc_final: 0.8121 (t70) REVERT: B 314 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8527 (m) REVERT: C 259 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: C 314 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8617 (m) REVERT: C 365 GLU cc_start: 0.7637 (mp0) cc_final: 0.7347 (mp0) REVERT: C 425 ASP cc_start: 0.7930 (t0) cc_final: 0.7659 (t0) REVERT: D 107 ASP cc_start: 0.8373 (t70) cc_final: 0.8119 (t70) REVERT: D 461 MET cc_start: 0.4204 (OUTLIER) cc_final: 0.3885 (ttt) outliers start: 36 outliers final: 16 residues processed: 222 average time/residue: 1.3645 time to fit residues: 358.2036 Evaluate side-chains 211 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 430 MET Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 461 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.9990 chunk 288 optimal weight: 0.6980 chunk 262 optimal weight: 4.9990 chunk 280 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 85 optimal weight: 0.0040 chunk 253 optimal weight: 7.9990 chunk 265 optimal weight: 0.5980 chunk 279 optimal weight: 1.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 25884 Z= 0.146 Angle : 0.423 4.894 35064 Z= 0.222 Chirality : 0.043 0.134 3960 Planarity : 0.003 0.025 4470 Dihedral : 6.833 59.928 3498 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.29 % Favored : 92.52 % Rotamer: Outliers : 1.09 % Allowed : 21.93 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 3156 helix: 0.88 (0.17), residues: 1104 sheet: -0.78 (0.23), residues: 588 loop : -1.26 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 290 HIS 0.004 0.001 HIS E 39 PHE 0.008 0.001 PHE E 225 TYR 0.012 0.001 TYR B 148 ARG 0.001 0.000 ARG B 37 *********************** 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 216 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 3.227 Fit side-chains revert: symmetry clash REVERT: A 314 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8567 (m) REVERT: F 259 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: F 314 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8618 (m) REVERT: F 365 GLU cc_start: 0.7590 (mp0) cc_final: 0.7362 (mp0) REVERT: E 107 ASP cc_start: 0.8363 (t70) cc_final: 0.8106 (t70) REVERT: B 107 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7669 (t70) REVERT: B 314 VAL cc_start: 0.8871 (OUTLIER) cc_final: 0.8565 (m) REVERT: C 259 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: C 314 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8643 (m) REVERT: C 365 GLU cc_start: 0.7590 (mp0) cc_final: 0.7287 (mp0) REVERT: C 425 ASP cc_start: 0.7962 (t0) cc_final: 0.7693 (t0) REVERT: D 107 ASP cc_start: 0.8374 (t70) cc_final: 0.8119 (t70) outliers start: 30 outliers final: 16 residues processed: 213 average time/residue: 1.2819 time to fit residues: 320.8920 Evaluate side-chains 208 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 3.9990 chunk 296 optimal weight: 7.9990 chunk 180 optimal weight: 0.1980 chunk 140 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 310 optimal weight: 5.9990 chunk 286 optimal weight: 5.9990 chunk 247 optimal weight: 0.0170 chunk 25 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 overall best weight: 2.2424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 25884 Z= 0.329 Angle : 0.535 5.123 35064 Z= 0.284 Chirality : 0.047 0.177 3960 Planarity : 0.004 0.029 4470 Dihedral : 7.344 59.653 3498 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.59 % Favored : 91.22 % Rotamer: Outliers : 1.09 % Allowed : 21.97 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3156 helix: 0.50 (0.17), residues: 1068 sheet: -0.97 (0.23), residues: 588 loop : -1.37 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 290 HIS 0.008 0.001 HIS A 228 PHE 0.013 0.002 PHE D 225 TYR 0.017 0.002 TYR F 174 ARG 0.003 0.000 ARG D 49 ********************** 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 194 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 2.956 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7769 (t70) REVERT: A 314 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8611 (m) REVERT: F 259 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: F 314 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8673 (m) REVERT: F 365 GLU cc_start: 0.7697 (mp0) cc_final: 0.7478 (mp0) REVERT: E 107 ASP cc_start: 0.8404 (t70) cc_final: 0.8138 (t70) REVERT: B 107 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7725 (t70) REVERT: B 314 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8607 (m) REVERT: C 259 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: C 365 GLU cc_start: 0.7713 (mp0) cc_final: 0.7493 (mp0) REVERT: C 425 ASP cc_start: 0.7900 (t0) cc_final: 0.7666 (t0) REVERT: D 107 ASP cc_start: 0.8413 (t70) cc_final: 0.8146 (t70) outliers start: 30 outliers final: 18 residues processed: 191 average time/residue: 1.4472 time to fit residues: 325.5925 Evaluate side-chains 185 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 271 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 7.9990 chunk 263 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 228 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 247 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 254 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN E 154 GLN ** E 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.150691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.112209 restraints weight = 35810.344| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.11 r_work: 0.3175 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 25884 Z= 0.233 Angle : 0.476 4.940 35064 Z= 0.253 Chirality : 0.045 0.162 3960 Planarity : 0.003 0.027 4470 Dihedral : 7.157 59.011 3498 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.83 % Favored : 91.98 % Rotamer: Outliers : 1.20 % Allowed : 21.75 % Favored : 77.05 % 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: -0.96 (0.16), residues: 3156 helix: 0.55 (0.17), residues: 1104 sheet: -0.98 (0.23), residues: 588 loop : -1.38 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 386 HIS 0.006 0.001 HIS A 228 PHE 0.010 0.001 PHE D 161 TYR 0.013 0.001 TYR E 148 ARG 0.002 0.000 ARG A 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7269.03 seconds wall clock time: 132 minutes 24.58 seconds (7944.58 seconds total)